# Modules & Global Variables

The Fortran modules found in the Tinker package are listed below along with a brief description of the variables associated with each module. Each individual module contains a set of globally allocated variables available to any program unit upon inclusion of that module. A source listing containing each of the Tinker functions and subroutines and its included modules can be produced by running the “listing.make” script found in the distribution.

ACTION Module total number of each energy term type

    neb             number of bond stretch energy terms computed
    nea             number of angle bend energy terms computed
    neba            number of stretch-bend energy terms computed
    neub            number of Urey-Bradley energy terms computed
    neaa            number of angle-angle energy terms computed
    neopb           number of out-of-plane bend energy terms computed
    neopd           number of out-of-plane distance energy terms computed
    neid            number of improper dihedral energy terms computed
    neit            number of improper torsion energy terms computed
    net             number of torsional energy terms computed
    nept            number of pi-system torsion energy terms computed
    nebt            number of stretch-torsion energy terms computed
    neat            number of angle-torsion energy terms computed
    nett            number of torsion-torsion energy terms computed
    nev             number of van der Waals energy terms computed
    ner             number of Pauli repulsion energy terms computed
    nedsp           number of dispersion energy terms computed
    nec             number of charge-charge energy terms computed
    necd            number of charge-dipole energy terms computed
    ned             number of dipole-dipole energy terms computed
    nem             number of multipole energy terms computed
    nep             number of polarization energy terms computed
    nect            number of charge transfer energy terms computed
    new             number of Ewald summation energy terms computed
    nerxf           number of reaction field energy terms computed
    nes             number of solvation energy terms computed
    nelf            number of metal ligand field energy terms computed
    neg             number of geometric restraint energy terms computed
    nex             number of extra energy terms computed

ALFMOL Module AlphaMol area and volume information

    alfthread       number of OpenMP threads to use for AlphaMol2
    delcxeps        eps value for AlphaMol Delaunay triangulation
    alfhydro        logical flag to include hydrogen atoms in AlphaMol
    alfsosgmp       logical flag governing use of SoS GMP in AlphaMol
    alfmethod       set AlphaMol1 or AlphaMol2 (SINGLE or MULTI threaded)
    alfsort         set sort method (NONE, Sort3D, BRIO, Split, KDTree)

ALIGN Module information for structure superposition

    nfit            number of atoms to use in superimposing two structures
    ifit            atom numbers of pairs of atoms to be superimposed
    wfit            weights assigned to atom pairs during superposition

ANALYZ Module energy components partitioned to atoms

    aesum           total potential energy partitioned over atoms
    aeb             bond stretch energy partitioned over atoms
    aea             angle bend energy partitioned over atoms
    aeba            stretch-bend energy partitioned over atoms
    aeub            Urey-Bradley energy partitioned over atoms
    aeaa            angle-angle energy partitioned over atoms
    aeopb           out-of-plane bend energy partitioned over atoms
    aeopd           out-of-plane distance energy partitioned over atoms
    aeid            improper dihedral energy partitioned over atoms
    aeit            improper torsion energy partitioned over atoms
    aet             torsional energy partitioned over atoms
    aept            pi-system torsion energy partitioned over atoms
    aebt            stretch-torsion energy partitioned over atoms
    aeat            angle-torsion energy partitioned over atoms
    aett            torsion-torsion energy partitioned over atoms
    aev             van der Waals energy partitioned over atoms
    aer             Pauli repulsion energy partitioned over atoms
    aedsp           damped dispersion energy partitioned over atoms
    aec             charge-charge energy partitioned over atoms
    aecd            charge-dipole energy partitioned over atoms
    aed             dipole-dipole energy partitioned over atoms
    aem             multipole energy partitioned over atoms
    aep             polarization energy partitioned over atoms
    aect            charge transfer energy partitioned over atoms
    aerxf           reaction field energy partitioned over atoms
    aes             solvation energy partitioned over atoms
    aelf            metal ligand field energy partitioned over atoms
    aeg             geometric restraint energy partitioned over atoms
    aex             extra energy term partitioned over atoms

ANGANG Module angle-angles in current structure

    nangang         total number of angle-angle interactions
    iaa             angle numbers used in each angle-angle term
    kaa             force constant for angle-angle cross terms

ANGBND Module bond angle bends in current structure

    nangle          total number of angle bends in the system
    iang            numbers of the atoms in each angle bend
    ak              harmonic angle force constant (kcal/mole/rad**2)
    anat            ideal bond angle or phase shift angle (degrees)
    afld            periodicity for Fourier angle bending term

ANGPOT Module angle bend functional form details

    angunit         convert angle bending energy to kcal/mole
    stbnunit        convert stretch-bend energy to kcal/mole
    aaunit          convert angle-angle energy to kcal/mole
    opbunit         convert out-of-plane bend energy to kcal/mole
    opdunit         convert out-of-plane distance energy to kcal/mole
    cang            cubic coefficient in angle bending potential
    qang            quartic coefficient in angle bending potential
    pang            quintic coefficient in angle bending potential
    sang            sextic coefficient in angle bending potential
    copb            cubic coefficient in out-of-plane bend potential
    qopb            quartic coefficient in out-of-plane bend potential
    popb            quintic coefficient in out-of-plane bend potential
    sopb            sextic coefficient in out-of-plane bend potential
    copd            cubic coefficient in out-of-plane distance potential
    qopd            quartic coefficient in out-of-plane distance potential
    popd            quintic coefficient in out-of-plane distance potential
    sopd            sextic coefficient in out-of-plane distance potential
    opbtyp          type of out-of-plane bend potential energy function
    angtyp          type of angle bending function for each bond angle

ANGTOR Module angle-torsions in current structure

    nangtor         total number of angle-torsion interactions
    iat             torsion and angle numbers used in angle-torsion
    kant            1-, 2- and 3-fold angle-torsion force constants

ARGUE Module command line arguments at run time

    maxarg          maximum number of command line arguments
    narg            number of command line arguments to the program
    listarg         flag to mark available command line arguments
    arg             strings containing the command line arguments

ASCII Module selected ASCII character code values

    null            decimal value of ASCII code for null (0)
    tab             decimal value of ASCII code for tab (9)
    linefeed        decimal value of ASCII code for linefeed (10)
    formfeed        decimal value of ASCII code for formfeed (12)
    carriage        decimal value of ASCII code for carriage return (13)
    escape          decimal value of ASCII code for escape (27)
    space           decimal value of ASCII code for blank space (32)
    exclamation     decimal value of ASCII code for exclamation (33)
    quote           decimal value of ASCII code for double quote (34)
    pound           decimal value of ASCII code for pound sign (35)
    dollar          decimal value of ASCII code for dollar sign (36)
    percent         decimal value of ASCII code for percent sign (37)
    ampersand       decimal value of ASCII code for ampersand (38)
    apostrophe      decimal value of ASCII code for single quote (39)
    asterisk        decimal value of ASCII code for asterisk (42)
    plus            decimal value of ASCII code for plus sign (43)
    comma           decimal value of ASCII code for comma (44)
    minus           decimal value of ASCII code for minus sign (45)
    period          decimal value of ASCII code for period (46)
    frontslash      decimal value of ASCII codd for frontslash (47)
    colon           decimal value of ASCII code for colon (58)
    semicolon       decimal value of ASCII code for semicolon (59)
    equal           decimal value of ASCII code for equal sign (61)
    question        decimal value of ASCII code for question mark (63)
    atsign          decimal value of ASCII code for at sign (64)
    backslash       decimal value of ASCII code for backslash (92)
    caret           decimal value of ASCII code for caret (94)
    underbar        decimal value of ASCII code for underbar (95)
    vertical        decimal value of ASCII code for vertical bar (124)
    tilde           decimal value of ASCII code for tilde (126)
    nbsp            decimal value of ASCII code for nobreak space (255)

ATMLST Module bond and angle local geometry indices

    bndlist         numbers of the bonds involving each atom
    anglist         numbers of the angles centered on each atom
    balist          numbers of the bonds comprising each angle

ATOMID Module atomic properties for current atoms

    tag             integer atom labels from input coordinates file
    class           atom class number for each atom in the system
    atomic          atomic number for each atom in the system
    valnum          valence number for each atom in the system
    mass            atomic weight for each atom in the system
    name            atom name for each atom in the system
    tier            tier name (residue, motif, etc.) for each atom
    story           descriptive type for each atom in the system

ATOMS Module number, position and type of atoms

    n               total number of atoms in the current system
    type            atom type number for each atom in the system
    x               current x-coordinate for each atom in the system
    y               current y-coordinate for each atom in the system
    z               current z-coordinate for each atom in the system

BATH Module thermostat and barostat control values

    maxnose         maximum length of Nose-Hoover thermostat chain
    voltrial        mean number of steps between Monte Carlo moves
    kelvin          target value for the system temperature (K)
    atmsph          target value for the system pressure (atm)
    tautemp         time constant for Berendsen thermostat (psec)
    taupres         time constant for Berendsen barostat (psec)
    compress        isothermal compressibility of medium (atm-1)
    collide         collision frequency for Andersen thermostat
    eta             velocity value for Bussi-Parrinello barostat
    volmove         maximum volume move for Monte Carlo barostat (Ang**3)
    vbar            velocity of log volume for Nose-Hoover barostat
    qbar            mass of the volume for Nose-Hoover barostat
    gbar            force for the volume for Nose-Hoover barostat
    vnh             velocity of each chained Nose-Hoover thermostat
    qnh             mass for each chained Nose-Hoover thermostat
    gnh             force for each chained Nose-Hoover thermostat
    isothermal      logical flag governing use of temperature control
    isobaric        logical flag governing use of pressure control
    prestyp         pressure control type (ISOTROPIC, SEMIISO or ANISO)
    volscale        choice of scaling method for Monte Carlo barostat
    thermostat      choice of temperature control method to be used
    barostat        choice of pressure control method to be used

BITOR Module bitorsions in the current structure

    nbitor          total number of bitorsions in the system
    ibitor          numbers of the atoms in each bitorsion

BNDPOT Module bond stretch functional form details

    cbnd            cubic coefficient in bond stretch potential
    qbnd            quartic coefficient in bond stretch potential
    bndunit         convert bond stretch energy to kcal/mole
    bndtyp          type of bond stretch potential energy function

BNDSTR Module bond stretches in the current structure

    nbond           total number of bond stretches in the system
    ibnd            numbers of the atoms in each bond stretch
    bk              bond stretch force constants (kcal/mole/Ang**2)
    bl              ideal bond length values in Angstroms

BOUND Module periodic boundary condition controls

    polycut         cutoff distance for infinite polymer nonbonds
    polycut2        square of infinite polymer nonbond cutoff
    use_bounds      flag to use periodic boundary conditions
    use_replica     flag to use replicates for periodic system
    use_polymer     flag to mark presence of infinite polymer
    use_wrap        flag to wrap coordinates in output files

BOXES Module periodic boundary condition parameters

    xbox            length of a-axis of periodic box in Angstroms
    ybox            length of b-axis of periodic box in Angstroms
    zbox            length of c-axis of periodic box in Angstroms
    alpha           angle between b- and c-axes of box in degrees
    beta            angle between a- and c-axes of box in degrees
    gamma           angle between a- and b-axes of box in degrees
    xbox2           half of the a-axis length of periodic box
    ybox2           half of the b-axis length of periodic box
    zbox2           half of the c-axis length of periodic box
    box34           three-fourths axis length of truncated octahedron
    volbox          volume in Ang**3 of the periodic box
    alpha_sin       sine of the alpha periodic box angle
    alpha_cos       cosine of the alpha periodic box angle
    beta_sin        sine of the beta periodic box angle
    beta_cos        cosine of the beta periodic box angle
    gamma_sin       sine of the gamma periodic box angle
    gamma_cos       cosine of the gamma periodic box angle
    beta_term       term used in generating triclinic box
    gamma_term      term used in generating triclinic box
    lvec            real space lattice vectors as matrix rows
    recip           reciprocal lattice vectors as matrix columns
    orthogonal      flag to mark periodic box as orthogonal
    monoclinic      flag to mark periodic box as monoclinic
    triclinic       flag to mark periodic box as triclinic
    octahedron      flag to mark box as truncated octahedron
    dodecadron      flag to mark box as rhombic dodecahedron
    nonprism        flag to mark octahedron or dodecahedron
    nosymm          flag to mark use or lack of lattice symmetry
    spacegrp        space group symbol for the unit cell type

CELL Module replicated cell periodic boundaries

    ncell           total number of cell replicates for periodic boundaries
    icell           offset along axes for each replicate periodic cell
    xcell           length of the a-axis of the complete replicated cell
    ycell           length of the b-axis of the complete replicated cell
    zcell           length of the c-axis of the complete replicated cell
    xcell2          half the length of the a-axis of the replicated cell
    ycell2          half the length of the b-axis of the replicated cell
    zcell2          half the length of the c-axis of the replicated cell

CFLUX Module charge flux terms in current system

    bflx            bond stretching charge flux constant (electrons/Ang)
    aflx            angle bending charge flux constant (electrons/radian)
    abflx           asymmetric stretch charge flux constant (electrons/Ang)

CHARGE Module partial charges in current structure

    nion            total number of partial charges in system
    iion            number of the atom site for each partial charge
    jion            neighbor generation site for each partial charge
    kion            cutoff switching site for each partial charge
    pchg            current atomic partial charge values (e-)
    pchg0           original partial charge values for charge flux

CHGPEN Module charge penetration in current structure

    ncp             total number of charge penetration sites in system
    pcore           number of core electrons at each multipole site
    pval            number of valence electrons at each multipole site
    pval0           original number of valence electrons for charge flux
    palpha          charge penetration damping at each multipole site

CHGPOT Module charge-charge functional form details

    electric        energy factor in kcal/mole for current force field
    dielec          dielectric constant for electrostatic interactions
    ebuffer         electrostatic buffering constant added to distance
    c1scale         factor by which 1-1 charge interactions are scaled
    c2scale         factor by which 1-2 charge interactions are scaled
    c3scale         factor by which 1-3 charge interactions are scaled
    c4scale         factor by which 1-4 charge interactions are scaled
    c5scale         factor by which 1-5 charge interactions are scaled
    neutnbr         logical flag governing use of neutral group neighbors
    neutcut         logical flag governing use of neutral group cutoffs

CHGTRN Module charge transfer for current structure

    nct             total number of dispersion sites in the system
    chgct           charge for charge transfer at each multipole site
    dmpct           charge transfer damping factor at each multipole site

CHRONO Module clock time values for current program

    twall           current processor wall clock time in seconds
    tcpu            elapsed cpu time from start of program in seconds

CHUNKS Module PME grid spatial decomposition values

    nchunk          total number of spatial regions for PME grid
    nchk1           number of spatial regions along the a-axis
    nchk2           number of spatial regions along the b-axis
    nchk3           number of spatial regions along the c-axis
    ngrd1           number of grid points per region along a-axis
    ngrd2           number of grid points per region along b-axis
    ngrd3           number of grid points per region along c-axis
    nlpts           PME grid points to the left of center point
    nrpts           PME grid points to the right of center point
    grdoff          offset for index into B-spline coefficients
    pmetable        PME grid spatial regions involved for each site

COUPLE Module atom neighbor connectivity lists

    n12             number of atoms directly bonded to each atom
    n13             number of atoms in a 1-3 relation to each atom
    n14             number of atoms in a 1-4 relation to each atom
    n15             number of atoms in a 1-5 relation to each atom
    i12             atom numbers of atoms 1-2 connected to each atom
    i13             atom numbers of atoms 1-3 connected to each atom
    i14             atom numbers of atoms 1-4 connected to each atom
    i15             atom numbers of atoms 1-5 connected to each atom

CTRPOT Module charge transfer functional form details

    ctrntyp         type of charge transfer term (SEPARATE or COMBINED)

DERIV Module Cartesian coord derivative components

    desum           total energy Cartesian coordinate derivatives
    deb             bond stretch Cartesian coordinate derivatives
    dea             angle bend Cartesian coordinate derivatives
    deba            stretch-bend Cartesian coordinate derivatives
    deub            Urey-Bradley Cartesian coordinate derivatives
    deaa            angle-angle Cartesian coordinate derivatives
    deopb           out-of-plane bend Cartesian coordinate derivatives
    deopd           out-of-plane distance Cartesian coordinate derivatives
    deid            improper dihedral Cartesian coordinate derivatives
    deit            improper torsion Cartesian coordinate derivatives
    det             torsional Cartesian coordinate derivatives
    dept            pi-system torsion Cartesian coordinate derivatives
    debt            stretch-torsion Cartesian coordinate derivatives
    deat            angle-torsion Cartesian coordinate derivatives
    dett            torsion-torsion Cartesian coordinate derivatives
    dev             van der Waals Cartesian coordinate derivatives
    der             Pauli repulsion Cartesian coordinate derivatives
    dedsp           damped dispersion Cartesian coordinate derivatives
    dec             charge-charge Cartesian coordinate derivatives
    decd            charge-dipole Cartesian coordinate derivatives
    ded             dipole-dipole Cartesian coordinate derivatives
    dem             multipole Cartesian coordinate derivatives
    dep             polarization Cartesian coordinate derivatives
    dect            charge transfer Cartesian coordinate derivatives
    derxf           reaction field Cartesian coordinate derivatives
    des             solvation Cartesian coordinate derivatives
    delf            metal ligand field Cartesian coordinate derivatives
    deg             geometric restraint Cartesian coordinate derivatives
    dex             extra energy term Cartesian coordinate derivatives

DIPOLE Module bond dipoles in current structure

    ndipole         total number of dipoles in the system
    idpl            numbers of atoms that define each dipole
    bdpl            magnitude of each of the dipoles (Debye)
    sdpl            position of each dipole between defining atoms

DISGEO Module distance geometry bounds & parameters

    vdwmax          maximum value of hard sphere sum for an atom pair
    compact         index of local distance compaction on embedding
    pathmax         maximum value of upper bound after smoothing
    dbnd            distance geometry upper and lower bounds matrix
    georad          hard sphere radii for distance geometry atoms
    use_invert      flag to use enantiomer closest to input structure
    use_anneal      flag to use simulated annealing refinement

DISP Module damped dispersion for current structure

    ndisp           total number of dispersion sites in the system
    idisp           number of the atom for each dispersion site
    csixpr          pairwise sum of C6 dispersion coefficients
    csix            C6 dispersion coefficient value at each site
    adisp           alpha dispersion damping value at each site

DMA Module QM spherical harmonic multipole moments

    mp              atomic monopole charge values from DMA
    dpx             atomic dipole moment x-component from DMA
    dpy             atomic dipole moment y-component from DMA
    dpz             atomic dipole moment z-component from DMA
    q20             atomic Q20 quadrupole component from DMA (zz)
    q21c            atomic Q21c quadrupole component from DMA (xz)
    q21s            atomic Q21s quadrupole component from DMA (yz)
    q22c            atomic Q22c quadrupole component from DMA (xx-yy)
    q22s            atomic Q22s quadrupole component from DMA (xy)

DOMEGA Module derivative components over torsions

    tesum           total energy derivatives over torsions
    teb             bond stretch derivatives over torsions
    tea             angle bend derivatives over torsions
    teba            stretch-bend derivatives over torsions
    teub            Urey-Bradley derivatives over torsions
    teaa            angle-angle derivatives over torsions
    teopb           out-of-plane bend derivatives over torsions
    teopd           out-of-plane distance derivatives over torsions
    teid            improper dihedral derivatives over torsions
    teit            improper torsion derivatives over torsions
    tet             torsional derivatives over torsions
    tept            pi-system torsion derivatives over torsions
    tebt            stretch-torsion derivatives over torsions
    teat            angle-torsion derivatives over torsions
    tett            torsion-torsion derivatives over torsions
    tev             van der Waals derivatives over torsions
    ter             Pauli repulsion derivatives over torsions
    tedsp           dampled dispersion derivatives over torsions
    tec             charge-charge derivatives over torsions
    tecd            charge-dipole derivatives over torsions
    ted             dipole-dipole derivatives over torsions
    tem             atomic multipole derivatives over torsions
    tep             polarization derivatives over torsions
    tect            charge transfer derivatives over torsions
    terxf           reaction field derivatives over torsions
    tes             solvation derivatives over torsions
    telf            metal ligand field derivatives over torsions
    teg             geometric restraint derivatives over torsions
    tex             extra energy term derivatives over torsions

DSPPOT Module dispersion interaction scale factors

    dsp2scale       scale factor for 1-2 dispersion energy interactions
    dsp3scale       scale factor for 1-3 dispersion energy interactions
    dsp4scale       scale factor for 1-4 dispersion energy interactions
    dsp5scale       scale factor for 1-5 dispersion energy interactions
    use_dcorr       flag to use long range dispersion correction

ENERGI Module individual potential energy components

    esum            total potential energy of the system
    eb              bond stretch potential energy of the system
    ea              angle bend potential energy of the system
    eba             stretch-bend potential energy of the system
    eub             Urey-Bradley potential energy of the system
    eaa             angle-angle potential energy of the system
    eopb            out-of-plane bend potential energy of the system
    eopd            out-of-plane distance potential energy of the system
    eid             improper dihedral potential energy of the system
    eit             improper torsion potential energy of the system
    et              torsional potential energy of the system
    ept             pi-system torsion potential energy of the system
    ebt             stretch-torsion potential energy of the system
    eat             angle-torsion potential energy of the system
    ett             torsion-torsion potential energy of the system
    ev              van der Waals potential energy of the system
    er              Pauli repulsion potential energy of the system
    edsp            dampled dispersion potential energy of the system
    ec              charge-charge potential energy of the system
    ecd             charge-dipole potential energy of the system
    ed              dipole-dipole potential energy of the system
    em              atomic multipole potential energy of the system
    ep              polarization potential energy of the system
    ect             charge transfer potential energy of the system
    erxf            reaction field potential energy of the system
    es              solvation potential energy of the system
    elf             metal ligand field potential energy of the system
    eg              geometric restraint potential energy of the system
    ex              extra term potential energy of the system

EWALD Module Ewald summation parameters and options

    aewald          current value of Ewald convergence coefficient
    aeewald         Ewald convergence coefficient for electrostatics
    apewald         Ewald convergence coefficient for polarization
    adewald         Ewald convergence coefficient for dispersion
    boundary        Ewald boundary condition; none, tinfoil or vacuum

EXPOL Module exch-polarization in current structure

    nexpol          total number of exch polarization sites in system
    kpep            exchange polarization spring constant at each site
    prepep          exchange polarization prefactor at each site
    dmppep          exchange polarization damping alpha at each site
    polscale        scale matrix for use in exchange polarization
    polinv          scale matrix inverse for exchange polarization
    lpep            flag to use exchange polarization at each site

EXTFLD Module applied external electric field vector

    exfld           components of applied external electric field
    use_exfld       flag to include applied external electric field

FACES Module Connolly area and volume variables

    maxcls          maximum number of neighboring atom pairs
    maxtt           maximum number of temporary tori
    maxt            maximum number of total tori
    maxp            maximum number of probe positions
    maxv            maximum number of vertices
    maxen           maximum number of concave edges
    maxfn           maximum number of concave faces
    maxc            maximum number of circles
    maxeq           maximum number of convex edges
    maxfs           maximum number of saddle faces
    maxfq           maximum number of convex faces
    maxcy           maximum number of cycles
    mxcyeq          maximum number of convex edge cycles
    mxfqcy          maximum number of convex face cycles
    na              number of atoms
    pr              probe radius
    ar              atomic radii
    axyz            atomic coordinates
    skip            if true, atom is not used
    nosurf          if true, atom has no free surface
    afree           atom free of neighbors
    abur            atom buried
    cls             atom numbers of neighbors
    clst            pointer from neighbor to torus
    acls            begin and end pointers for atoms neighbors
    ntt             number of temporary tori
    ttfe            first edge of each temporary torus
    ttle            last edge of each temporary torus
    enext           pointer to next edge of temporary torus
    tta             temporary torus atom numbers
    ttbur           temporary torus buried
    ttfree          temporary torus free
    nt              number of tori
    tfe             torus first edge
    ta              torus atom numbers
    tr              torus radius
    t               torus center
    tax             torus axis
    tfree           torus free of neighbors
    np              number of probe positions
    pa              probe position atom numbers
    p               probe position coordinates
    nv              number of vertices
    va              vertex atom number
    vp              vertex probe number
    vxyz            vertex coordinates
    nen             number of concave edges
    nfn             number of concave faces
    env             vertex numbers for each concave edge
    fnen            concave face concave edge numbers
    nc              number of circles
    ca              circle atom number
    ct              circle torus number
    cr              circle radius
    c               circle center
    neq             number of convex edges
    eqc             convex edge circle number
    eqv             convex edge vertex numbers
    afe             first convex edge of each atom
    ale             last convex edge of each atom
    eqnext          pointer to next convex edge of atom
    nfs             number of saddle faces
    fsen            saddle face concave edge numbers
    fseq            saddle face convex edge numbers
    ncy             number of cycles
    cyneq           number of convex edges in cycle
    cyeq            cycle convex edge numbers
    nfq             number of convex faces
    fqa             atom number of convex face
    fqncy           number of cycles bounding convex face
    fqcy            convex face cycle numbers

FFT Module Fast Fourier transform control values

    maxprime        maximum number of prime factors of FFT dimension
    iprime          prime factorization of each FFT dimension (FFTPACK)
    planf           pointer to forward transform data structure (FFTW)
    planb           pointer to backward transform data structure (FFTW)
    ffttable        intermediate array used by the FFT routine (FFTPACK)
    ffttyp          type of FFT package; currently FFTPACK or FFTW

FIELDS Module molecular mechanics force field type

    biotyp          force field atom type of each biopolymer type
    forcefield      string used to describe the current forcefield

FILES Module name & number of current structure file

    nprior          number of previously existing cycle files
    ldir            length in characters of the directory name
    leng            length in characters of the base filename
    filename        fill filename including any extension or version
    outfile         output filename used for intermediate results

FRACS Module distances to molecular center of mass

    xfrac           fractional coordinate along a-axis of center of mass
    yfrac           fractional coordinate along b-axis of center of mass
    zfrac           fractional coordinate along c-axis of center of mass

FREEZE Module definition of holonomic constraints

    nrat            number of holonomic distance constraints to apply
    nratx           number of atom group holonomic constraints to apply
    nwat            number of rigid three- and four-site water molecules
    nwat4           number of rigid planar four-site water molecules
    iratx           group number for each group holonomic constraint
    kratx           spatial constraint type (1=plane, 2=line, 3=point)
    irat            atom numbers of atoms in each holonomic constraint
    iwat            atom numbers of O and H atoms in each rigid water
    iwat4           atom numbers involved in each rigid four-site water
    rateps          convergence tolerance for holonomic constraints
    krat            ideal distance value for each holonomic constraint
    kwat            ideal distances for O-H and H-H in rigid water
    kwat4           linear scaling values to build four-site water
    use_freeze      logical flag to set use of holonomic contraints
    frzimage        flag to use minimum image for holonomic constraint

GKSTUF Module generalized Kirkwood solvation values

    gkc             tuning parameter exponent in the f(GB) function
    gkr             generalized Kirkwood cavity radii for atom types

GROUP Module partitioning of system into atom groups

    ngrp            total number of atom groups in the system
    kgrp            contiguous list of the atoms in each group
    grplist         number of the group to which each atom belongs
    igrp            first and last atom of each group in the list
    grpmass         total mass of all the atoms in each group
    wgrp            weight for each set of group-group interactions
    use_group       flag to use partitioning of system into groups
    use_intra       flag to include only intragroup interactions
    use_inter       flag to include only intergroup interactions

HESCUT Module cutoff for Hessian matrix elements

    hesscut         magnitude of smallest allowed Hessian element

HESSN Module Cartesian Hessian elements for one atom

    hessx           Hessian elements for x-component of current atom
    hessy           Hessian elements for y-component of current atom
    hessz           Hessian elements for z-component of current atom

HPMF Module hydrophobic potential of mean force term

    rcarbon         radius of a carbon atom for use with HPMF
    rwater          radius of a water molecule for use with HPMF
    acsurf          surface area of a hydrophobic carbon atom
    safact          constant for calculation of atomic surface area
    tgrad           tanh slope (set very steep, default=100)
    toffset         shift the tanh plot along the x-axis (default=6)
    hpmfcut         cutoff distance for pairwise HPMF interactions
    hd1             hd2,hd3  hydrophobic PMF well depth parameter
    hc1             hc2,hc3  hydrophobic PMF well center point
    hw1             hw2,hw3  reciprocal of the hydrophobic PMF well width
    npmf            number of hydrophobic carbon atoms in the system
    ipmf            number of the atom for each HPMF carbon atom site
    rpmf            radius of each atom for use with hydrophobic PMF
    acsa            SASA value for each hydrophobic PMF carbon atom

IELSCF Module extended Lagrangian induced dipoles

    nfree_aux       total degrees of freedom for auxiliary dipoles
    tautemp_aux     time constant for auxiliary Berendsen thermostat
    kelvin_aux      target system temperature for auxiliary dipoles
    uaux            auxiliary induced dipole value at each site
    upaux           auxiliary shadow induced dipoles at each site
    vaux            auxiliary induced dipole velocity at each site
    vpaux           auxiliary shadow dipole velocity at each site
    aaux            auxiliary induced dipole acceleration at each site
    apaux           auxiliary shadow dipole acceleration at each site
    use_ielscf      flag to use inertial extended Lagrangian method

IMPROP Module improper dihedrals in current structure

    niprop          total number of improper dihedral angles in the system
    iiprop          numbers of the atoms in each improper dihedral angle
    kprop           force constant values for improper dihedral angles
    vprop           ideal improper dihedral angle value in degrees

IMPTOR Module improper torsions in current structure

    nitors          total number of improper torsional angles in the system
    iitors          numbers of the atoms in each improper torsional angle
    itors1          1-fold amplitude and phase for each improper torsion
    itors2          2-fold amplitude and phase for each improper torsion
    itors3          3-fold amplitude and phase for each improper torsion

INFORM Module program I/O and flow control values

    maxask          maximum number of queries for interactive input
    gpucard         integer flag for GPU use (0=no GPU, 1=GPU present)
    digits          decimal places output for energy and coordinates
    iprint          steps between status printing (0=no printing)
    iwrite          steps between coordinate saves (0=no saves)
    isend           steps between socket communication (0=no sockets)
    verbose         logical flag to turn on extra information printing
    debug           logical flag to turn on extensive debug printing
    silent          logical flag to turn off all information printing
    holdup          logical flag to wait for carriage return on exit
    abort           logical flag to stop execution at next chance

INTER Module sum of intermolecular energy components

    einter          total intermolecular potential energy

IOUNIT Module Fortran input/output unit numbers

    input           Fortran I/O unit for main input (default=5)
    iout            Fortran I/O unit for main output (default=6)

KANANG Module angle-angle term forcefield parameters

    anan            angle-angle cross term parameters for each atom class

KANGS Module bond angle bend forcefield parameters

    maxna           maximum number of harmonic angle bend parameter entries
    maxna5          maximum number of 5-membered ring angle bend entries
    maxna4          maximum number of 4-membered ring angle bend entries
    maxna3          maximum number of 3-membered ring angle bend entries
    maxnap          maximum number of in-plane angle bend parameter entries
    maxnaf          maximum number of Fourier angle bend parameter entries
    acon            force constant parameters for harmonic angle bends
    acon5           force constant parameters for 5-ring angle bends
    acon4           force constant parameters for 4-ring angle bends
    acon3           force constant parameters for 3-ring angle bends
    aconp           force constant parameters for in-plane angle bends
    aconf           force constant parameters for Fourier angle bends
    ang             bond angle parameters for harmonic angle bends
    ang5            bond angle parameters for 5-ring angle bends
    ang4            bond angle parameters for 4-ring angle bends
    ang3            bond angle parameters for 3-ring angle bends
    angp            bond angle parameters for in-plane angle bends
    angf            phase shift angle and periodicity for Fourier bends
    ka              string of atom classes for harmonic angle bends
    ka5             string of atom classes for 5-ring angle bends
    ka4             string of atom classes for 4-ring angle bends
    ka3             string of atom classes for 3-ring angle bends
    kap             string of atom classes for in-plane angle bends
    kaf             string of atom classes for Fourier angle bends

KANTOR Module angle-torsion forcefield parameters

    maxnat          maximum number of angle-torsion parameter entries
    atcon           torsional amplitude parameters for angle-torsion
    kat             string of atom classes for angle-torsion terms

KATOMS Module atom definition forcefield parameters

    atmcls          atom class number for each of the atom types
    atmnum          atomic number for each of the atom types
    ligand          number of atoms to be attached to each atom type
    weight          average atomic mass of each atom type
    symbol          modified atomic symbol for each atom type
    describe        string identifying each of the atom types

KBONDS Module bond stretching forcefield parameters

    maxnb           maximum number of bond stretch parameter entries
    maxnb5          maximum number of 5-membered ring bond stretch entries
    maxnb4          maximum number of 4-membered ring bond stretch entries
    maxnb3          maximum number of 3-membered ring bond stretch entries
    maxnel          maximum number of electronegativity bond corrections
    bcon            force constant parameters for harmonic bond stretch
    bcon5           force constant parameters for 5-ring bond stretch
    bcon4           force constant parameters for 4-ring bond stretch
    bcon3           force constant parameters for 3-ring bond stretch
    blen            bond length parameters for harmonic bond stretch
    blen5           bond length parameters for 5-ring bond stretch
    blen4           bond length parameters for 4-ring bond stretch
    blen3           bond length parameters for 3-ring bond stretch
    dlen            electronegativity bond length correction parameters
    kb              string of atom classes for harmonic bond stretch
    kb5             string of atom classes for 5-ring bond stretch
    kb4             string of atom classes for 4-ring bond stretch
    kb3             string of atom classes for 3-ring bond stretch
    kel             string of atom classes for electronegativity corrections

KCHRGE Module partial charge forcefield parameters

    chg             partial charge parameters for each atom type

KCPEN Module charge penetration forcefield parameters

    cpele           valence electron magnitude for each atom class
    cpalp           alpha charge penetration parameter for each atom class

KCTRN Module charge transfer forcefield parameters

    ctchg           charge transfer magnitude for each atom class
    ctdmp           alpha charge transfer parameter for each atom class

KDIPOL Module bond dipole forcefield parameters

    maxnd           maximum number of bond dipole parameter entries
    maxnd5          maximum number of 5-membered ring dipole entries
    maxnd4          maximum number of 4-membered ring dipole entries
    maxnd3          maximum number of 3-membered ring dipole entries
    dpl             dipole moment parameters for bond dipoles
    dpl5            dipole moment parameters for 5-ring dipoles
    dpl4            dipole moment parameters for 4-ring dipoles
    dpl3            dipole moment parameters for 3-ring dipoles
    pos             dipole position parameters for bond dipoles
    pos5            dipole position parameters for 5-ring dipoles
    pos4            dipole position parameters for 4-ring dipoles
    pos3            dipole position parameters for 3-ring dipoles
    kd              string of atom classes for bond dipoles
    kd5             string of atom classes for 5-ring dipoles
    kd4             string of atom classes for 4-ring dipoles
    kd3             string of atom classes for 3-ring dipoles

KDSP Module damped dispersion forcefield parameters

    dspsix          C6 dispersion coefficient for each atom class
    dspdmp          alpha dispersion parameter for each atom class

KEXPL Module exch-polarization forcefield parameters

    pepk            exchange-polarization spring constant for atom classes
    peppre          exchange-polarization prefactor for atom classes
    pepdmp          exchange-polarization damping alpha for atom classes
    pepl            exchange-polarization logical flag for atom classes

KEYS Module contents of the keyword control file

    maxkey          maximum number of lines in the keyword file
    nkey            number of nonblank lines in the keyword file
    keyline         contents of each individual keyword file line

KHBOND Module H-bonding term forcefield parameters

    maxnhb          maximum number of hydrogen bonding pair entries
    radhb           radius parameter for hydrogen bonding pairs
    epshb           well depth parameter for hydrogen bonding pairs
    khb             string of atom types for hydrogen bonding pairs

KIPROP Module improper dihedral forcefield parameters

    maxndi          maximum number of improper dihedral parameter entries
    dcon            force constant parameters for improper dihedrals
    tdi             ideal dihedral angle values for improper dihedrals
    kdi             string of atom classes for improper dihedral angles

KITORS Module improper torsion forcefield parameters

    maxnti          maximum number of improper torsion parameter entries
    ti1             torsional parameters for improper 1-fold rotation
    ti2             torsional parameters for improper 2-fold rotation
    ti3             torsional parameters for improper 3-fold rotation
    kti             string of atom classes for improper torsional parameters

KMULTI Module atomic multipole forcefield parameters

    maxnmp          maximum number of atomic multipole parameter entries
    multip          atomic monopole, dipole and quadrupole values
    mpaxis          type of local axis definition for atomic multipoles
    kmp             string of atom types for atomic multipoles

KOPBND Module out-of-plane bend forcefield parameters

    maxnopb         maximum number of out-of-plane bending entries
    opbn            force constant parameters for out-of-plane bending
    kopb            string of atom classes for out-of-plane bending

KOPDST Module out-of-plane distance forcefield params

    maxnopd         maximum number of out-of-plane distance entries
    opds            force constant parameters for out-of-plane distance
    kopd            string of atom classes for out-of-plane distance

KORBS Module pisystem orbital forcefield parameters

    maxnpi          maximum number of pisystem bond parameter entries
    maxnpi5         maximum number of 5-membered ring pibond entries
    maxnpi4         maximum number of 4-membered ring pibond entries
    sslope          slope for bond stretch vs. pi-bond order
    sslope5         slope for 5-ring bond stretch vs. pi-bond order
    sslope4         slope for 4-ring bond stretch vs. pi-bond order
    tslope          slope for 2-fold torsion vs. pi-bond order
    tslope5         slope for 5-ring 2-fold torsion vs. pi-bond order
    tslope4         slope for 4-ring 2-fold torsion vs. pi-bond order
    electron        number of pi-electrons for each atom class
    ionize          ionization potential for each atom class
    repulse         repulsion integral value for each atom class
    kpi             string of atom classes for pisystem bonds
    kpi5            string of atom classes for 5-ring pisystem bonds
    kpi4            string of atom classes for 4-ring pisystem bonds

KPITOR Module pi-system torsion forcefield parameters

    maxnpt          maximum number of pi-system torsion parameter entries
    ptcon           force constant parameters for pi-system torsions
    kpt             string of atom classes for pi-system torsion terms

KPOLPR Module special Thole forcefield parameters

    maxnpp          maximum number of special pair polarization entries
    thlpr           Thole damping values for special polarization pairs
    thdpr           Thole direct damping for special polarization pairs
    kppr            string of atom types for special polarization pairs

KPOLR Module polarizability forcefield parameters

    pgrp            connected types in polarization group of each atom type
    polr            dipole polarizability parameters for each atom type
    athl            Thole polarizability damping value for each atom type
    dthl            alternate Thole direct polarization damping values

KREPL Module Pauli repulsion forcefield parameters

    prsiz           Pauli repulsion size value for each atom class
    prdmp           alpha Pauli repulsion parameter for each atom class
    prele           number of valence electrons for each atom class

KSOLUT Module solvation term forcefield parameters

    pbr             Poisson-Boltzmann radius value for each atom type
    csr             ddCOSMO solvation radius value for each atom type
    gkr             Generalized Kirkwood radius value for each atom type
    snk             neck correction scale factor for each atom type

KSTBND Module stretch-bend forcefield parameters

    maxnsb          maximum number of stretch-bend parameter entries
    stbn            force constant parameters for stretch-bend terms
    ksb             string of atom classes for stretch-bend terms

KSTTOR Module stretch-torsion forcefield parameters

    maxnbt          maximum number of stretch-torsion parameter entries
    btcon           torsional amplitude parameters for stretch-torsion
    kbt             string of atom classes for stretch-torsion terms

KTORSN Module torsional angle forcefield parameters

    maxnt           maximum number of torsional angle parameter entries
    maxnt5          maximum number of 5-membered ring torsion entries
    maxnt4          maximum number of 4-membered ring torsion entries
    t1              torsional parameters for standard 1-fold rotation
    t2              torsional parameters for standard 2-fold rotation
    t3              torsional parameters for standard 3-fold rotation
    t4              torsional parameters for standard 4-fold rotation
    t5              torsional parameters for standard 5-fold rotation
    t6              torsional parameters for standard 6-fold rotation
    t15             torsional parameters for 1-fold rotation in 5-ring
    t25             torsional parameters for 2-fold rotation in 5-ring
    t35             torsional parameters for 3-fold rotation in 5-ring
    t45             torsional parameters for 4-fold rotation in 5-ring
    t55             torsional parameters for 5-fold rotation in 5-ring
    t65             torsional parameters for 6-fold rotation in 5-ring
    t14             torsional parameters for 1-fold rotation in 4-ring
    t24             torsional parameters for 2-fold rotation in 4-ring
    t34             torsional parameters for 3-fold rotation in 4-ring
    t44             torsional parameters for 4-fold rotation in 4-ring
    t54             torsional parameters for 5-fold rotation in 4-ring
    t64             torsional parameters for 6-fold rotation in 4-ring
    kt              string of atom classes for torsional angles
    kt5             string of atom classes for 5-ring torsions
    kt4             string of atom classes for 4-ring torsions

KTRTOR Module torsion-torsion forcefield parameters

    maxntt          maximum number of torsion-torsion parameter entries
    maxtgrd         maximum dimension of torsion-torsion spline grid
    maxtgrd2        maximum number of torsion-torsion spline grid points
    tnx             number of columns in torsion-torsion spline grid
    tny             number of rows in torsion-torsion spline grid
    ttx             angle values for first torsion of spline grid
    tty             angle values for second torsion of spline grid
    tbf             function values at points on spline grid
    tbx             gradient over first torsion of spline grid
    tby             gradient over second torsion of spline grid
    tbxy            Hessian cross components over spline grid
    ktt             string of torsion-torsion atom classes

KURYBR Module Urey-Bradley term forcefield parameters

    maxnu           maximum number of Urey-Bradley parameter entries
    ucon            force constant parameters for Urey-Bradley terms
    dst13           ideal 1-3 distance parameters for Urey-Bradley terms
    ku              string of atom classes for Urey-Bradley terms

KVDWPR Module special pair vdw forcefield parameters

    maxnvp          maximum number of special van der Waals pair entries
    radpr           radius parameter for special van der Waals pairs
    epspr           well depth parameter for special van der Waals pairs
    kvpr            string of atom classes for special van der Waals pairs

KVDWS Module van der Waals term forcefield parameters

    rad             van der Waals radius parameter for each atom class
    eps             van der Waals well depth parameter for each atom class
    rad4            van der Waals radius parameter in 1-4 interactions
    eps4            van der Waals well depth parameter in 1-4 interactions
    reduct          van der Waals reduction factor for each atom class

LIGHT Module method of lights pair neighbors indices

    nlight          total number of sites for method of lights calculation
    kbx             low index of neighbors of each site in the x-sorted list
    kby             low index of neighbors of each site in the y-sorted list
    kbz             low index of neighbors of each site in the z-sorted list
    kex             high index of neighbors of each site in the x-sorted list
    key             high index of neighbors of each site in the y-sorted list
    kez             high index of neighbors of each site in the z-sorted list
    locx            maps the x-sorted list into original interaction list
    locy            maps the y-sorted list into original interaction list
    locz            maps the z-sorted list into original interaction list
    rgx             maps the original interaction list into x-sorted list
    rgy             maps the original interaction list into y-sorted list
    rgz             maps the original interaction list into z-sorted list

LIMITS Module interaction taper & cutoff distances

    vdwcut          cutoff distance for van der Waals interactions
    repcut          cutoff distance for Pauli repulsion interactions
    dispcut         cutoff distance for dispersion interactions
    chgcut          cutoff distance for charge-charge interactions
    dplcut          cutoff distance for dipole-dipole interactions
    mpolecut        cutoff distance for atomic multipole interactions
    ctrncut         cutoff distance for charge transfer interactions
    vdwtaper        distance at which van der Waals switching begins
    reptaper        distance at which Pauli repulsion switching begins
    disptaper       distance at which dispersion switching begins
    chgtaper        distance at which charge-charge switching begins
    dpltaper        distance at which dipole-dipole switching begins
    mpoletaper      distance at which atomic multipole switching begins
    ctrntaper       distance at which charge transfer switching begins
    ewaldcut        cutoff distance for real space Ewald electrostatics
    dewaldcut       cutoff distance for real space Ewald dispersion
    usolvcut        cutoff distance for dipole solver preconditioner
    use_ewald       logical flag governing use of electrostatic Ewald
    use_dewald      logical flag governing use of dispersion Ewald
    use_lights      logical flag governing use of method of lights
    use_list        logical flag governing use of any neighbor lists
    use_vlist       logical flag governing use of van der Waals list
    use_dlist       logical flag governing use of dispersion list
    use_clist       logical flag governing use of charge list
    use_mlist       logical flag governing use of multipole list
    use_ulist       logical flag governing use of preconditioner list

LINMIN Module line search minimization parameters

    intmax          maximum number of interpolations during line search
    stpmin          minimum step length in current line search direction
    stpmax          maximum step length in current line search direction
    cappa           stringency of line search (0=tight < cappa < 1=loose)
    slpmax          projected gradient above which stepsize is reduced
    angmax          maximum angle between search direction and -gradient

MATH Module mathematical and geometrical constants

    pi              numerical value of the geometric constant
    elog            numerical value of the natural logarithm base
    radian          conversion factor from radians to degrees
    logten          numerical value of the natural log of ten
    twosix          numerical value of the sixth root of two
    sqrtpi          numerical value of the square root of Pi
    sqrttwo         numerical value of the square root of two
    sqrtthree       numerical value of the square root of three

MDSTUF Module molecular dynamics trajectory controls

    nfree           total number of degrees of freedom for a system
    irest           steps between removal of COM motion (0=no removal)
    bmnmix          mixing coefficient for use with Beeman integrator
    nrespa          inner steps per outer step for RESPA integrator
    arespa          inner time step for use with RESPA integrator
    dorest          logical flag to remove center of mass motion
    integrate       type of molecular dynamics integration algorithm

MERCK Module MMFF-specific force field parameters

    nlignes         number of atom pairs having MMFF Bond Type 1
    bt_1            atom pairs having MMFF Bond Type 1
    eqclass         table of atom class equivalencies used to find
    default         parameters if explicit values are missing
    see             J. Comput. Chem., 17, 490-519, '95, Table IV)
    crd             number of attached neighbors    |
    val             valency value                   |  see T. A. Halgren,
    pilp            if 0, no lone pair              |  J. Comput. Chem.,
    if              1, one or more lone pair(s)  |  17, 616-645 (1995)
    mltb            multibond indicator             |
    arom            aromaticity indicator           |
    lin             linearity indicator             |
    sbmb            single- vs multiple-bond flag   |
    mmffarom        aromatic rings parameters
    mmffaromc       cationic aromatic rings parameters
    mmffaroma       anionic aromatic rings parameters

MINIMA Module general parameters for minimizations

    nextiter        iteration number to use for the first iteration
    fctmin          value below which function is deemed optimized
    hguess          initial value for the H-matrix diagonal elements
    maxiter         maximum number of iterations during optimization

MOLCUL Module individual molecules in current system

    nmol            total number of separate molecules in the system
    imol            first and last atom of each molecule in the list
    kmol            contiguous list of the atoms in each molecule
    molcule         number of the molecule to which each atom belongs
    totmass         total weight of all the molecules in the system
    molmass         molecular weight for each molecule in the system

MOLDYN Module MD trajectory velocity & acceleration

    v               current velocity of each atom along the x,y,z-axes
    a               current acceleration of each atom along x,y,z-axes
    aalt            alternate acceleration of each atom along x,y,z-axes

MOMENT Module electric multipole moment components

    netchg          net electric charge for the total system
    netdpl          dipole moment magnitude for the total system
    netqdp          diagonal quadrupole (Qxx, Qyy, Qzz) for system
    xdpl            dipole vector x-component in the global frame
    ydpl            dipole vector y-component in the global frame
    zdpl            dipole vector z-component in the global frame
    xxqdp           quadrupole tensor xx-component in global frame
    xyqdp           quadrupole tensor xy-component in global frame
    xzqdp           quadrupole tensor xz-component in global frame
    yxqdp           quadrupole tensor yx-component in global frame
    yyqdp           quadrupole tensor yy-component in global frame
    yzqdp           quadrupole tensor yz-component in global frame
    zxqdp           quadrupole tensor zx-component in global frame
    zyqdp           quadrupole tensor zy-component in global frame
    zzqdp           quadrupole tensor zz-component in global frame

MPLPOT Module multipole functional form details

    m2scale         scale factor for 1-2 multipole energy interactions
    m3scale         scale factor for 1-3 multipole energy interactions
    m4scale         scale factor for 1-4 multipole energy interactions
    m5scale         scale factor for 1-5 multipole energy interactions
    use_chgpen      flag to use charge penetration damped potential
    pentyp          type of penetration damping (NONE, GORDON1, GORDON2)

MPOLE Module atomic multipoles in current structure

    maxpole         max components (monopole=1,dipole=4,quadrupole=13)
    npole           total number of multipole sites in the system
    ipole           number of the atom for each multipole site
    polsiz          number of multipole components at each atom
    pollist         multipole site for each atom (0=no multipole)
    zaxis           number of the z-axis defining atom for each atom
    xaxis           number of the x-axis defining atom for each atom
    yaxis           number of the y-axis defining atom for each atom
    pole            local frame Cartesian multipoles for each atom
    rpole           global frame Cartesian multipoles for each atom
    mono0           original atomic monopole values for charge flux
    polaxe          local coordinate frame type for each atom

MRECIP Module reciprocal PME for permanent multipoles

    vmxx            scalar sum xx-component of virial due to multipoles
    vmyy            scalar sum yy-component of virial due to multipoles
    vmzz            scalar sum zz-component of virial due to multipoles
    vmxy            scalar sum xy-component of virial due to multipoles
    vmxz            scalar sum xz-component of virial due to multipoles
    vmyz            scalar sum yz-component of virial due to multipoles
    cmp             Cartesian permenent multipoles as polytensor vector
    fmp             fractional permanent multipoles as polytensor vector
    cphi            Cartesian permanent multipole potential and field
    fphi            fractional permanent multipole potential and field

MUTANT Module free energy calculation hybrid atoms

    nmut            number of atoms mutated from initial to final state
    vcouple         van der Waals lambda type (0=decouple, 1=annihilate)
    imut            atomic sites differing in initial and final state
    type0           atom type of each atom in the initial state system
    class0          atom class of each atom in the initial state system
    type1           atom type of each atom in the final state system
    class1          atom class of each atom in the final state system
    lambda          generic weighting between initial and final states
    vlambda         state weighting value for van der Waals potentials
    elambda         state weighting value for electrostatic potentials
    tlambda         state weighting value for torsional potential
    scexp           scale factor for soft core buffered 14-7 potential
    scalpha         scale factor for soft core buffered 14-7 potential
    mut             true if an atom is to be mutated, false otherwise

NEIGH Module pairwise neighbor list indices & storage

    maxvlst         maximum size of van der Waals pair neighbor lists
    maxelst         maximum size of electrostatic pair neighbor lists
    maxulst         maximum size of dipole preconditioner pair lists
    nvlst           number of sites in list for each vdw site
    vlst            site numbers in neighbor list of each vdw site
    nelst           number of sites in list for each electrostatic site
    elst            site numbers in list of each electrostatic site
    nulst           number of sites in list for each preconditioner site
    ulst            site numbers in list of each preconditioner site
    lbuffer         width of the neighbor list buffer region
    pbuffer         width of the preconditioner list buffer region
    lbuf2           square of half the neighbor list buffer width
    pbuf2           square of half the preconditioner list buffer width
    vbuf2           square of van der Waals cutoff plus the list buffer
    vbufx           square of van der Waals cutoff plus 2X list buffer
    dbuf2           square of dispersion cutoff plus the list buffer
    dbufx           square of dispersion cutoff plus 2X list buffer
    cbuf2           square of charge cutoff plus the list buffer
    cbufx           square of charge cutoff plus 2X list buffer
    mbuf2           square of multipole cutoff plus the list buffer
    mbufx           square of multipole cutoff plus 2X list buffer
    ubuf2           square of preconditioner cutoff plus the list buffer
    ubufx           square of preconditioner cutoff plus 2X list buffer
    xvold           x-coordinate at last vdw/dispersion list update
    yvold           y-coordinate at last vdw/dispersion list update
    zvold           z-coordinate at last vdw/dispersion list update
    xeold           x-coordinate at last electrostatic list update
    yeold           y-coordinate at last electrostatic list update
    zeold           z-coordinate at last electrostatic list update
    xuold           x-coordinate at last preconditioner list update
    yuold           y-coordinate at last preconditioner list update
    zuold           z-coordinate at last preconditioner list update
    dovlst          logical flag to rebuild vdw neighbor list
    dodlst          logical flag to rebuild dispersion neighbor list
    doclst          logical flag to rebuild charge neighbor list
    domlst          logical flag to rebuild multipole neighbor list
    doulst          logical flag to rebuild preconditioner neighbor list

NONPOL Module nonpolar cavity & dispersion parameters

    epso            water oxygen eps for implicit dispersion term
    epsh            water hydrogen eps for implicit dispersion term
    rmino           water oxygen Rmin for implicit dispersion term
    rminh           water hydrogen Rmin for implicit dispersion term
    awater          water number density at standard temp & pressure
    slevy           enthalpy-to-free energy scale factor for dispersion
    shctd           HCT overlap scale factor for the dispersion integral
    dspoff          radius offset for the start of dispersion integral
    cavprb          probe radius for use in computing cavitation energy
    solvprs         limiting microscopic solvent pressure value
    surften         limiting macroscopic surface tension value
    spcut           starting radius for solvent pressure tapering
    spoff           cutoff radius for solvent pressure tapering
    stcut           starting radius for surface tension tapering
    stoff           cutoff radius for surface tension tapering
    radcav          atomic radius of each atom for cavitation energy
    raddsp          atomic radius of each atom for dispersion energy
    epsdsp          vdw well depth of each atom for dispersion energy
    cdisp           maximum dispersion energy for each atom

NUCLEO Module parameters for nucleic acid structure

    pucker          sugar pucker, either 2=2'-endo or 3=3'-endo
    glyco           glycosidic torsional angle for each nucleotide
    bkbone          phosphate backbone angles for each nucleotide
    dblhlx          flag to mark system as nucleic acid double helix
    deoxy           flag to mark deoxyribose or ribose sugar units
    hlxform         helix form (A, B or Z) of polynucleotide strands

OMEGA Module torsional space dihedral angle values

    nomega          number of dihedral angles allowed to rotate
    iomega          numbers of two atoms defining rotation axis
    zline           line number in Z-matrix of each dihedral angle
    dihed           current value in radians of each dihedral angle

OPBEND Module out-of-plane bends in current structure

    nopbend         total number of out-of-plane bends in the system
    iopb            bond angle numbers used in out-of-plane bending
    opbk            force constant values for out-of-plane bending

OPDIST Module out-of-plane distances in structure

    nopdist         total number of out-of-plane distances in the system
    iopd            numbers of the atoms in each out-of-plane distance
    opdk            force constant values for out-of-plane distance

OPENMP Module OpenMP processor and thread values

    nproc           number of processors available to OpenMP
    nthread         number of threads to be used with OpenMP
    nnest           number of nested active parallel regions

ORBITS Module conjugated pisystem orbital energies

    qorb            number of pi-electrons contributed by each atom
    worb            ionization potential of each pisystem atom
    emorb           repulsion integral for each pisystem atom

OUTPUT Module output file format control parameters

    archive         logical flag for coordinates in Tinker XYZ format
    binary          logical flag for coordinates in DCD binary format
    noversion       logical flag governing use of filename versions
    overwrite       logical flag to overwrite intermediate files inplace
    arcsave         logical flag to save coordinates in Tinker XYZ format
    dcdsave         logical flag to save coordinates in DCD binary format
    cyclesave       logical flag to mark use of numbered cycle files
    velsave         logical flag to save velocity vector components
    frcsave         logical flag to save force vector components
    uindsave        logical flag to save induced atomic dipoles
    coordtype       selects Cartesian, internal, rigid body or none

PARAMS Module force field parameter file contents

    maxprm          maximum number of lines in the parameter file
    nprm            number of nonblank lines in the parameter file
    prmline         contents of each individual parameter file line

PATHS Module Elber reaction path method parameters

    pnorm           length of the reactant-product vector
    acoeff          transformation matrix 'A' from Elber algorithm
    pc0             reactant Cartesian coordinates as variables
    pc1             product Cartesian coordinates as variables
    pvect           vector connecting the reactant and product
    pstep           step per cycle along reactant-product vector
    pzet            current projection on reactant-product vector
    gc              gradient of the path constraints

PBSTUF Module Poisson-Boltzmann solvation parameters

APBS configuration parameters (see APBS documentation for details). In the column on the right are possible values for each variable, with default values given in brackets. Only a subset of the APBS options are supported and/or are appropriate for use with AMOEBA.

    pbtyp           lpbe
    pbsoln          mg-auto, [mg-manual]
    bcfl            boundary conditions              zero, sdh, [mdh]
    chgm            multipole discretization         spl4
    srfm            surface method                   mol, smol, [spl4]
    dime            number of grid points            [65, 65, 65]
    grid            grid spacing (mg-manual)         fxn of "dime"
    cgrid           coarse grid spacing              fxn of "dime"
    fgrid           fine grid spacing                cgrid / 2
    gcent           grid center (mg-manual)          center of mass
    cgcent          coarse grid center               center of mass
    fgcent          fine grid center                 center of mass
    pdie            solute/homogeneous dieletric     [1.0]
    sdie            solvent dieletric                [78.3]
    ionn            number of ion species            [0]
    ionc            ion concentration (M)            [0.0]
    ionq            ion charge (electrons)           [1.0]
    ionr            ion radius (A)                   [2.0]
    srad            solvent probe radius (A)         [1.4]
    swin            surface spline window width      [0.3]
    sdens           density of surface points        [10.0]
    smin            minimum distance between an      [10.0]
    pbe             Poisson-Boltzmann permanent multipole solvation energy
    apbe            Poisson-Boltzmann permanent multipole energy over atoms
    pbr             Poisson-Boltzmann cavity radii for atom types
    pbep            Poisson-Boltzmann energies on permanent multipoles
    pbfp            Poisson-Boltzmann forces on permanent multipoles
    pbtp            Poisson-Boltzmann torques on permanent multipoles
    pbeuind         Poisson-Boltzmann field due to induced dipoles
    pbeuinp         Poisson-Boltzmann field due to non-local induced dipoles

PDB Module Protein Data Bank structure definition

    npdb            number of atoms stored in Protein Data Bank format
    nres            number of residues stored in Protein Data Bank format
    nmodel          number of models stored in Protein Data Bank format
    imodel          model number of structure to be used (0=All Models)
    resnum          number of the residue to which each atom belongs
    resatm          number of first and last atom in each residue
    npdb12          number of atoms directly bonded to each CONECT atom
    ipdb12          atom numbers of atoms connected to each CONECT atom
    pdbmod          Protein Data Bank model number assigned to each atom
    pdblist         list of the Protein Data Bank atom number of each atom
    xpdb            x-coordinate of each atom stored in PDB format
    ypdb            y-coordinate of each atom stored in PDB format
    zpdb            z-coordinate of each atom stored in PDB format
    altsym          string with PDB alternate locations to be included
    pdbtyp          format of PDB files; PDB (legacy) or CIF (PDBx/mmCIF)
    pdbres          Protein Data Bank residue name assigned to each atom
    pdbsym          Protein Data Bank atomic symbol assigned to each atom
    pdbatm          Protein Data Bank atom name assigned to each atom
    pdbrec          Protein Data Bank record type assigned to each atom
    chnsym          string with PDB chain identifiers to be included
    instyp          string with PDB insertion records to be included

PHIPSI Module phi-psi-omega-chi angles for protein

    chiral          chirality of each amino acid residue (1=L, -1=D)
    disulf          residue joined to each residue via a disulfide link
    phi             value of the phi angle for each amino acid residue
    psi             value of the psi angle for each amino acid residue
    omg             value of the omega angle for each amino acid residue
    chi             values of the chi angles for each amino acid residue

PIORBS Module conjugated system in current structure

    norbit          total number of pisystem orbitals in the system
    nconj           total number of separate conjugated piystems
    reorbit         number of evaluations between orbital updates
    nbpi            total number of bonds affected by the pisystem
    ntpi            total number of torsions affected by the pisystem
    iorbit          numbers of the atoms containing pisystem orbitals
    iconj           first and last atom of each pisystem in the list
    kconj           contiguous list of atoms in each pisystem
    piperp          atoms defining a normal plane to each orbital
    ibpi            bond and piatom numbers for each pisystem bond
    itpi            torsion and pibond numbers for each pisystem torsion
    pbpl            pi-bond orders for bonds in "planar" pisystem
    pnpl            pi-bond orders for bonds in "nonplanar" pisystem
    listpi          atom list indicating whether each atom has an orbital

PISTUF Module bond order-related pisystem parameters

    bkpi            bond stretch force constants for pi-bond order of 1.0
    blpi            ideal bond length values for a pi-bond order of 1.0
    kslope          rate of force constant decrease with bond order decrease
    lslope          rate of bond length increase with a bond order decrease
    torsp2          2-fold torsional energy barrier for pi-bond order of 1.0

PITORS Module pi-system torsions in current structure

    npitors         total number of pi-system torsional interactions
    ipit            numbers of the atoms in each pi-system torsion
    kpit            2-fold pi-system torsional force constants

PME Module values for particle mesh Ewald summation

    nfft1           current number of PME grid points along a-axis
    nfft2           current number of PME grid points along b-axis
    nfft3           current number of PME grid points along c-axis
    nefft1          number of grid points along electrostatic a-axis
    nefft2          number of grid points along electrostatic b-axis
    nefft3          number of grid points along electrostatic c-axis
    ndfft1          number of grid points along dispersion a-axis
    ndfft2          number of grid points along dispersion b-axis
    ndfft3          number of grid points along dispersion c-axis
    bsorder         current order of the PME B-spline values
    bseorder        order of the electrostatic PME B-spline values
    bsporder        order of the polarization PME B-spline values
    bsdorder        order of the dispersion PME B-spline values
    igrid           initial Ewald grid values for B-spline
    bsmod1          B-spline moduli along the a-axis direction
    bsmod2          B-spline moduli along the b-axis direction
    bsmod3          B-spline moduli along the c-axis direction
    bsbuild         B-spline derivative coefficient temporary storage
    thetai1         B-spline coefficients along the a-axis
    thetai2         B-spline coefficients along the b-axis
    thetai3         B-spline coefficients along the c-axis
    qgrid           values on the particle mesh Ewald grid
    qfac            prefactors for the particle mesh Ewald grid

POLAR Module induced dipole moments & polarizability

    npolar          total number of polarizable sites in the system
    ipolar          number of the atom for each polarizable site
    jpolar          index into polarization parameter matrix for each atom
    polarity        dipole polarizability for each atom site (Ang**3)
    thole           Thole polarization damping value for each atom
    tholed          Thole direct polarization damping value for each atom
    pdamp           value of polarizability scale factor for each atom
    thlval          Thole damping parameter value for each atom type pair
    thdval          alternate Thole direct damping value for atom type pair
    udir            direct induced dipole components for each atom site
    udirp           direct induced dipoles in field used for energy terms
    udirs           direct GK or PB induced dipoles for each atom site
    udirps          direct induced dipoles in field used for GK or PB energy
    uind            mutual induced dipole components for each atom site
    uinp            mutual induced dipoles in field used for energy terms
    uinds           mutual GK or PB induced dipoles for each atom site
    uinps           mutual induced dipoles in field used for GK or PB energy
    uexact          exact SCF induced dipoles to full numerical precision
    douind          flag to allow induced dipoles at each atom site

POLGRP Module polarization group connectivity lists

    maxp11          maximum number of atoms in a polarization group
    maxp12          maximum number of atoms in groups 1-2 to an atom
    maxp13          maximum number of atoms in groups 1-3 to an atom
    maxp14          maximum number of atoms in groups 1-4 to an atom
    np11            number of atoms in polarization group of each atom
    np12            number of atoms in groups 1-2 to each atom
    np13            number of atoms in groups 1-3 to each atom
    np14            number of atoms in groups 1-4 to each atom
    ip11            atom numbers of atoms in same group as each atom
    ip12            atom numbers of atoms in groups 1-2 to each atom
    ip13            atom numbers of atoms in groups 1-3 to each atom
    ip14            atom numbers of atoms in groups 1-4 to each atom

POLOPT Module induced dipoles for OPT extrapolation

    maxopt          maximum order for OPT induced dipole extrapolation
    optorder        highest coefficient order for OPT dipole extrapolation
    optlevel        current OPT order for reciprocal potential and field
    copt            coefficients for OPT total induced dipole moments
    copm            coefficients for OPT incremental induced dipole moments
    uopt            OPT induced dipole components at each multipole site
    uoptp           OPT induced dipoles in field used for energy terms
    uopts           OPT GK or PB induced dipoles at each multipole site
    uoptps          OPT induced dipoles in field used for GK or PB energy
    fopt            OPT fractional reciprocal potentials at multipole sites
    foptp           OPT fractional reciprocal potentials for energy terms

POLPCG Module induced dipoles via the PCG solver

    mindex          index into preconditioner inverse for PCG solver
    pcgpeek         value of acceleration factor for PCG peek step
    minv            preconditioner inverse for induced dipole PCG solver
    pcgprec         flag to allow use of preconditioner with PCG solver
    pcgguess        flag to use initial PCG based on direct field

POLPOT Module polarization functional form details

    politer         maximum number of induced dipole SCF iterations
    poleps          induced dipole convergence criterion (rms Debye/atom)
    p2scale         scale factor for 1-2 polarization energy interactions
    p3scale         scale factor for 1-3 polarization energy interactions
    p4scale         scale factor for 1-4 polarization energy interactions
    p5scale         scale factor for 1-5 polarization energy interactions
    p2iscale        scale factor for 1-2 intragroup polarization energy
    p3iscale        scale factor for 1-3 intragroup polarization energy
    p4iscale        scale factor for 1-4 intragroup polarization energy
    p5iscale        scale factor for 1-5 intragroup polarization energy
    d1scale         scale factor for intra-group direct induction
    d2scale         scale factor for 1-2 group direct induction
    d3scale         scale factor for 1-3 group direct induction
    d4scale         scale factor for 1-4 group direct induction
    u1scale         scale factor for intra-group mutual induction
    u2scale         scale factor for 1-2 group mutual induction
    u3scale         scale factor for 1-3 group mutual induction
    u4scale         scale factor for 1-4 group mutual induction
    w2scale         scale factor for 1-2 induced dipole interactions
    w3scale         scale factor for 1-3 induced dipole interactions
    w4scale         scale factor for 1-4 induced dipole interactions
    w5scale         scale factor for 1-5 induced dipole interactions
    udiag           acceleration factor for induced dipole SCF iterations
    dpequal         flag to set dscale values equal to pscale values
    use_thole       flag to use Thole damped polarization interactions
    use_tholed      flag to use alternate Thole for direct polarization
    use_expol       flag to use damped exchange polarization correction
    poltyp          type of polarization (MUTUAL, DIRECT, OPT or TCG)

POLTCG Module induced dipoles via the TCG solver

    tcgorder        total number of TCG iterations to be used
    tcgnab          number of mutual induced dipole components
    tcgpeek         value of acceleration factor for TCG peek step
    uad             left-hand side mutual induced d-dipoles
    uap             left-hand side mutual induced p-dipoles
    ubd             right-hand side mutual induced d-dipoles
    ubp             right-hand side mutual induced p-dipoles
    tcgguess        flag to use initial TCG based on direct field

POTENT Module usage of potential energy components

    use_bond        logical flag governing use of bond stretch potential
    use_angle       logical flag governing use of angle bend potential
    use_strbnd      logical flag governing use of stretch-bend potential
    use_urey        logical flag governing use of Urey-Bradley potential
    use_angang      logical flag governing use of angle-angle cross term
    use_opbend      logical flag governing use of out-of-plane bend term
    use_opdist      logical flag governing use of out-of-plane distance
    use_improp      logical flag governing use of improper dihedral term
    use_imptor      logical flag governing use of improper torsion term
    use_tors        logical flag governing use of torsional potential
    use_pitors      logical flag governing use of pi-system torsion term
    use_strtor      logical flag governing use of stretch-torsion term
    use_angtor      logical flag governing use of angle-torsion term
    use_tortor      logical flag governing use of torsion-torsion term
    use_vdw         logical flag governing use of van der Waals potential
    use_repel       logical flag governing use of Pauli repulsion term
    use_disp        logical flag governing use of dispersion potential
    use_charge      logical flag governing use of charge-charge potential
    use_chgdpl      logical flag governing use of charge-dipole potential
    use_dipole      logical flag governing use of dipole-dipole potential
    use_mpole       logical flag governing use of multipole potential
    use_polar       logical flag governing use of polarization term
    use_chgtrn      logical flag governing use of charge transfer term
    use_chgflx      logical flag governing use of charge flux term
    use_rxnfld      logical flag governing use of reaction field term
    use_solv        logical flag governing use of continuum solvation term
    use_metal       logical flag governing use of ligand field term
    use_geom        logical flag governing use of geometric restraints
    use_extra       logical flag governing use of extra potential term
    use_born        logical flag governing use of Born radii values
    use_orbit       logical flag governing use of pisystem computation
    use_mutate      logical flag governing use of hybrid potential terms

POTFIT Module values for electrostatic potential fit

    nconf           total number of configurations to be analyzed
    namax           maximum number of atoms in the largest configuration
    ngatm           total number of atoms with active potential grid points
    nfatm           total number of atoms in electrostatic potential fit
    npgrid          total number of electrostatic potential grid points
    ipgrid          atom associated with each potential grid point
    resp            weight used to restrain parameters to original values
    xdpl0           target x-component of molecular dipole moment
    ydpl0           target y-component of molecular dipole moment
    zdpl0           target z-component of molecular dipole moment
    xxqdp0          target xx-component of molecular quadrupole moment
    xyqdp0          target xy-component of molecular quadrupole moment
    xzqdp0          target xz-component of molecular quadrupole moment
    yyqdp0          target yy-component of molecular quadrupole moment
    yzqdp0          target yz-component of molecular quadrupole moment
    zzqdp0          target zz-component of molecular quadrupole moment
    fit0            initial value of each parameter used in potential fit
    fchg            partial charges by atom type during potential fit
    fpol            atomic multipoles by atom type during potential fit
    pgrid           Cartesian coordinates of potential grid points
    epot            values of electrostatic potential at grid points
    use_dpl         flag to include molecular dipole in potential fit
    use_qdp         flag to include molecular quadrupole in potential fit
    fit_mpl         flag for atomic monopoles to vary in potential fit
    fit_dpl         flag for atomic dipoles to vary in potential fit
    fit_qdp         flag for atomic quadrupoles to vary in potential fit
    fit_chgpen      flag for charge penetration to vary in potential fit
    fitchg          flag marking atom types used in partial charge fit
    fitpol          flag marking atom types used in atomic multipole fit
    fitcpen         flag marking atom types used in charge penetration
    gatm            flag to use potential grid points around each atom
    fatm            flag to use each atom in electrostatic potential fit
    vchg            flag for partial charge at each atom in fitting
    vpol            flag for atomic multipoles at each atom in fitting
    vcpen           flag for charge penetration at each atom in fitting
    resptyp         electrostatic restraint target (ORIG, ZERO or NONE)
    varpot          descriptive name for each variable in potential fit

PTABLE Module symbols and info for chemical elements

    maxele          maximum number of elements from periodic table
    atmass          standard atomic weight for each chemical element
    vdwrad          van der Waals radius for each chemical element
    covrad          covalent radius for each chemical element
    elemnt          atomic symbol for each chemical element

REFER Module reference atomic coordinate storage

    nref            total number of atoms in each reference system
    refltitle       length in characters of reference title lines
    refleng         length in characters of reference base filenames
    reftyp          atom types of the atoms in each reference system
    n12ref          number of atoms bonded to each reference atom
    i12ref          atom numbers of atoms 1-2 connected to each atom
    xboxref         reference a-axis length of periodic box
    yboxref         reference b-axis length of periodic box
    zboxref         reference c-axis length of periodic box
    alpharef        reference angle between b- and c-axes of box
    betaref         reference angle between a- and c-axes of box
    gammaref        reference angle between a- and b-axes of box
    xref            reference x-coordinates for atoms in each system
    yref            reference y-coordinates for atoms in each system
    zref            reference z-coordinates for atoms in each system
    refnam          atom names of the atoms in each reference system
    reffile         full filename for each reference system
    reftitle        title used to describe each reference system

REPEL Module Pauli repulsion for current structure

    nrep            total number of repulsion sites in the system
    irep            number of the atom for each repulsion site
    replist         repulsion multipole site for each atom (0=none)
    sizpr           Pauli repulsion size parameter value for each atom
    dmppr           Pauli repulsion alpha damping value for each atom
    elepr           Pauli repulsion valence electrons for each atom
    repole          repulsion Cartesian multipoles in the local frame
    rrepole         repulsion Cartesian multipoles in the global frame

REPPOT Module repulsion interaction scale factors

    r2scale         scale factor for 1-2 repulsion energy interactions
    r3scale         scale factor for 1-3 repulsion energy interactions
    r4scale         scale factor for 1-4 repulsion energy interactions
    r5scale         scale factor for 1-5 repulsion energy interactions

RESDUE Module amino acid & nucleotide residue names

    maxamino        maximum number of amino acid residue types
    maxnuc          maximum number of nucleic acid residue types
    ntyp            biotypes for mid-chain peptide backbone N atoms
    catyp           biotypes for mid-chain peptide backbone CA atoms
    ctyp            biotypes for mid-chain peptide backbone C atoms
    hntyp           biotypes for mid-chain peptide backbone HN atoms
    otyp            biotypes for mid-chain peptide backbone O atoms
    hatyp           biotypes for mid-chain peptide backbone HA atoms
    cbtyp           biotypes for mid-chain peptide backbone CB atoms
    nntyp           biotypes for N-terminal peptide backbone N atoms
    cantyp          biotypes for N-terminal peptide backbone CA atoms
    cntyp           biotypes for N-terminal peptide backbone C atoms
    hnntyp          biotypes for N-terminal peptide backbone HN atoms
    ontyp           biotypes for N-terminal peptide backbone O atoms
    hantyp          biotypes for N-terminal peptide backbone HA atoms
    nctyp           biotypes for C-terminal peptide backbone N atoms
    cactyp          biotypes for C-terminal peptide backbone CA atoms
    cctyp           biotypes for C-terminal peptide backbone C atoms
    hnctyp          biotypes for C-terminal peptide backbone HN atoms
    octyp           biotypes for C-terminal peptide backbone O atoms
    hactyp          biotypes for C-terminal peptide backbone HA atoms
    o5typ           biotypes for nucleotide backbone and sugar O5' atoms
    c5typ           biotypes for nucleotide backbone and sugar C5' atoms
    h51typ          biotypes for nucleotide backbone and sugar H5' atoms
    h52typ          biotypes for nucleotide backbone and sugar H5'' atoms
    c4typ           biotypes for nucleotide backbone and sugar C4' atoms
    h4typ           biotypes for nucleotide backbone and sugar H4' atoms
    o4typ           biotypes for nucleotide backbone and sugar O4' atoms
    c1typ           biotypes for nucleotide backbone and sugar C1' atoms
    h1typ           biotypes for nucleotide backbone and sugar H1' atoms
    c3typ           biotypes for nucleotide backbone and sugar C3' atoms
    h3typ           biotypes for nucleotide backbone and sugar H3' atoms
    c2typ           biotypes for nucleotide backbone and sugar C2' atoms
    h21typ          biotypes for nucleotide backbone and sugar H2' atoms
    o2typ           biotypes for nucleotide backbone and sugar O2' atoms
    h22typ          biotypes for nucleotide backbone and sugar H2'' atoms
    o3typ           biotypes for nucleotide backbone and sugar O3' atoms
    ptyp            biotypes for nucleotide backbone and sugar P atoms
    optyp           biotypes for nucleotide backbone and sugar OP atoms
    h5ttyp          biotypes for nucleotide backbone and sugar H5T atoms
    h3ttyp          biotypes for nucleotide backbone and sugar H3T atoms
    amino           three-letter abbreviations for amino acids types
    nuclz           three-letter abbreviations for nucleic acids types
    amino1          one-letter abbreviations for amino acids types
    nuclz1          one-letter abbreviations for nucleic acids types

RESTRN Module parameters for geometrical restraints

    npfix           number of position restraints to be applied
    ndfix           number of distance restraints to be applied
    nafix           number of angle restraints to be applied
    ntfix           number of torsional restraints to be applied
    ngfix           number of group distance restraints to be applied
    nchir           number of chirality restraints to be applied
    ipfix           atom number involved in each position restraint
    kpfix           flags to use x-, y-, z-coordinate position restraints
    idfix           atom numbers defining each distance restraint
    iafix           atom numbers defining each angle restraint
    itfix           atom numbers defining each torsional restraint
    igfix           group numbers defining each group distance restraint
    ichir           atom numbers defining each chirality restraint
    depth           depth of shallow Gaussian basin restraint
    width           exponential width coefficient of Gaussian basin
    rwall           radius of spherical droplet boundary restraint
    xpfix           x-coordinate target for each restrained position
    ypfix           y-coordinate target for each restrained position
    zpfix           z-coordinate target for each restrained position
    pfix            force constant and flat-well range for each position
    dfix            force constant and target range for each distance
    afix            force constant and target range for each angle
    tfix            force constant and target range for each torsion
    gfix            force constant and target range for each group distance
    chir            force constant and target range for chiral centers
    use_basin       logical flag governing use of Gaussian basin
    use_wall        logical flag governing use of droplet boundary

RGDDYN Module rigid body MD velocities and momenta

    xcmo            x-component from each atom to center of rigid body
    ycmo            y-component from each atom to center of rigid body
    zcmo            z-component from each atom to center of rigid body
    vcm             current translational velocity of each rigid body
    wcm             current angular velocity of each rigid body
    lm              current angular momentum of each rigid body
    vc              half-step translational velocity for kinetic energy
    wc              half-step angular velocity for kinetic energy
    linear          logical flag to mark group as linear or nonlinear

RIGID Module rigid body coordinates for atom groups

    xrb             rigid body reference x-coordinate for each atom
    yrb             rigid body reference y-coordinate for each atom
    zrb             rigid body reference z-coordinate for each atom
    rbc             current rigid body coordinates for each group
    use_rigid       flag to mark use of rigid body coordinate system

RING Module number and location of ring structures

    nring3          total number of 3-membered rings in the system
    nring4          total number of 4-membered rings in the system
    nring5          total number of 5-membered rings in the system
    nring6          total number of 6-membered rings in the system
    nring7          total number of 7-membered rings in the system
    iring3          numbers of the atoms involved in each 3-ring
    iring4          numbers of the atoms involved in each 4-ring
    iring5          numbers of the atoms involved in each 5-ring
    iring6          numbers of the atoms involved in each 6-ring
    iring7          numbers of the atoms involved in each 7-ring

ROTBND Module molecule partitions for bond rotation

    nrot            total number of atoms moving when bond rotates
    rot             atom numbers of atoms moving when bond rotates
    use_short       logical flag governing use of shortest atom list

RXNFLD Module reaction field matrix and indices

    ijk             indices into the reaction field element arrays
    b1              first reaction field matrix element array
    b2              second reaction field matrix element array

RXNPOT Module reaction field functional form details

    rfsize          radius of reaction field sphere centered at origin
    rfbulkd         bulk dielectric constant of reaction field continuum
    rfterms         number of terms to use in reaction field summation

SCALES Module optimization parameter scale factors

    scale           multiplicative factor for each optimization parameter
    set_scale       logical flag to show if scale factors have been set

SEQUEN Module sequence information for biopolymer

    nseq            total number of residues in biopolymer sequences
    nchain          number of separate biopolymer sequence chains
    ichain          first and last residue in each biopolymer chain
    seqtyp          residue type for each residue in the sequence
    seqatm          base atom number for each residue (Calpha or C4')
    chnnam          one-letter identifier for each sequence chain
    seq             three-letter code for each residue in the sequence
    chntyp          contents of each chain (GENERIC, PEPTIDE or NUCLEIC)

SHAPES Module UnionBall area and volume variables

    maxedge         maximum number of edges between ball centers
    maxtetra        maximum number of tetrahedra in the system
    npoint          total number of balls (points) in the system
    nvertex         total number of vertices in the system
    ntetra          total number of tetrahedra in the system
    nnew            total number of entries on new tetrahedra list
    nfree           total number of spaces on free tetrahedra list
    nkill           total number of tetrahedra on list to kill
    nlinkfacet      total number of triangle facets in the system
    newlist         list with index numbers of the new tetrahedra
    freespace       list of the tetrahedra currently in free space
    killspace       list of the existing tetrahedra to be killed
    vinfo           information value for each of the vertices
    tedge           number of an edge found in each tetrahedron
    tinfo           orientation information for each tetrahedron
    tnindex         index related to tetrahedron orientation
    tetra           numbers of the four balls in each tetrahedron
    tneighbor       store the four neighbors of each tetrahedron
    linkfacet       numbers of two tetrahedra defining each facet
    linkindex       vertex numbers opposite each facet triangle
    epsln2          minimal value of determinant over two balls
    epsln3          minimal value of determinant over three balls
    epsln4          minimal value of determinant over four balls
    epsln5          minimal value of determinant over five balls
    crdball         coordinates in Angstroms of balls as 1-D array
    radball         radius value for each ball in Angstroms
    wghtball        weight value assigned for each ball

SHUNT Module polynomial switching function values

    off             distance at which the potential energy goes to zero
    off2            square of distance at which the potential goes to zero
    cut             distance at which switching of the potential begins
    cut2            square of distance at which the switching begins
    c0              zeroth order coefficient of multiplicative switch
    c1              first order coefficient of multiplicative switch
    c2              second order coefficient of multiplicative switch
    c3              third order coefficient of multiplicative switch
    c4              fourth order coefficient of multiplicative switch
    c5              fifth order coefficient of multiplicative switch
    f0              zeroth order coefficient of additive switch function
    f1              first order coefficient of additive switch function
    f2              second order coefficient of additive switch function
    f3              third order coefficient of additive switch function
    f4              fourth order coefficient of additive switch function
    f5              fifth order coefficient of additive switch function
    f6              sixth order coefficient of additive switch function
    f7              seventh order coefficient of additive switch function

SIZES Module parameters to set array dimensions

    maxatm          maximum number of atoms in the molecular system
    maxtyp          maximum number of force field atom type definitions
    maxclass        maximum number of force field atom class definitions
    maxval          maximum number of atoms directly bonded to an atom
    maxref          maximum number of stored reference molecular systems
    maxgrp          maximum number of user-defined groups of atoms
    maxres          maximum number of residues in the macromolecule
    maxfix          maximum number of geometric constraints and restraints
    maxbio          maximum number of biopolymer atom definitions

SOCKET Module socket communication control parameters

    skttyp          socket information type (1=DYN, 2=OPT)
    cstep           current dynamics or optimization step number
    cdt             current dynamics cumulative simulation time
    cenergy         current potential energy from simulation
    sktstart        logical flag to indicate socket initialization
    sktstop         logical flag to indicate socket shutdown
    use_socket      logical flag governing use of external sockets

SOLPOT Module solvation term functional form details

    solvtyp         type of continuum solvation energy model in use
    borntyp         method to be used for the Born radius computation

SOLUTE Module continuum solvation model parameters

    doffset         dielectric offset to continuum solvation atomic radii
    onipr           probe radius to use with onion Born radius method
    p1              single-atom scale factor for analytical Still radii
    p2              1-2 interaction scale factor for analytical Still radii
    p3              1-3 interaction scale factor for analytical Still radii
    p4              nonbonded scale factor for analytical Still radii
    p5              soft cutoff parameter for analytical Still radii
    descoff         offset for pairwise descreening at small separation
    rneck           atom radius bins used to store Aij/Bij neck constants
    aneck           constants to use in calculating neck values
    bneck           constants to use in calculating neck values
    rsolv           atomic radius of each atom for continuum solvation
    rdescr          atomic radius of each atom for descreening
    asolv           atomic surface area solvation parameters
    rborn           Born radius of each atom for GB/SA solvation
    drb             solvation derivatives with respect to Born radii
    drbp            GK polarization derivatives with respect to Born radii
    drobc           chain rule term for Onufriev-Bashford-Case radii
    gpol            polarization self-energy values for each atom
    shct            overlap scale factors for Hawkins-Cramer-Truhlar radii
    aobc            alpha values for Onufriev-Bashford-Case radii
    bobc            beta values for Onufriev-Bashford-Case radii
    gobc            gamma values for Onufriev-Bashford-Case radii
    vsolv           atomic volume of each atom for use with ACE
    wace            "omega" values for atom class pairs for use with ACE
    s2ace           "sigma^2" values for atom class pairs for use with ACE
    uace            "mu" values for atom class pairs for use with ACE
    sneck           pairwise neck correction scale factor for each atom
    bornint         unscaled 1/r^6 corrections for tanh chain rule term
    useneck         logical flag to use neck interstitial space correction
    usetanh         logical flag to use tanh interstitial space correction

STODYN Module SD trajectory frictional coefficients

    friction        global frictional coefficient for exposed particle
    fgamma          atomic frictional coefficients for each atom
    use_sdarea      logical flag to use surface area friction scaling

STRBND Module stretch-bends in current structure

    nstrbnd         total number of stretch-bend interactions
    isb             angle and bond numbers used in stretch-bend
    sbk             force constants for stretch-bend terms

STRTOR Module stretch-torsions in current structure

    nstrtor         total number of stretch-torsion interactions
    ist             torsion and bond numbers used in stretch-torsion
    kst             1-, 2- and 3-fold stretch-torsion force constants

SYNTRN Module synchronous transit path definition

    tpath           value of the path coordinate (0=reactant, 1=product)
    ppath           path coordinate for extra point in quadratic transit
    xmin1           reactant coordinates as array of optimization variables
    xmin2           product coordinates as array of optimization variables
    xm              extra coordinate set for quadratic synchronous transit

TARRAY Module store dipole-dipole matrix elements

    ntpair          number of stored dipole-dipole matrix elements
    tindex          index into stored dipole-dipole matrix values
    tdipdip         stored dipole-dipole matrix element values

TETTOR Module tetratorsions in the current structure

    ntettor         total number of tetratorsions in the system
    itettor         numbers of the atoms in each tetratorsion

TORPOT Module torsional functional form details

    idihunit        convert improper dihedral energy to kcal/mole
    itorunit        convert improper torsion amplitudes to kcal/mole
    torsunit        convert torsional parameter amplitudes to kcal/mole
    ptorunit        convert pi-system torsion energy to kcal/mole
    storunit        convert stretch-torsion energy to kcal/mole
    atorunit        convert angle-torsion energy to kcal/mole
    ttorunit        convert torsion-torsion energy to kcal/mole

TORS Module torsional angles in current structure

    ntors           total number of torsional angles in the system
    itors           numbers of the atoms in each torsional angle
    tors1           1-fold amplitude and phase for each torsional angle
    tors2           2-fold amplitude and phase for each torsional angle
    tors3           3-fold amplitude and phase for each torsional angle
    tors4           4-fold amplitude and phase for each torsional angle
    tors5           5-fold amplitude and phase for each torsional angle
    tors6           6-fold amplitude and phase for each torsional angle

TORTOR Module torsion-torsions in current structure

    ntortor         total number of torsion-torsion interactions
    itt             atoms and parameter indices for torsion-torsion

TREE Module potential smoothing search tree levels

    maxpss          maximum number of potential smoothing levels
    nlevel          number of levels of potential smoothing used
    etree           energy reference value at the top of the tree
    ilevel          smoothing deformation value at each tree level

TRITOR Module tritorsions in the current structure

    ntritor         total number of tritorsions in the system
    itritor         numbers of the atoms in each tritorsion

UNITS Module physical constants and unit conversions

    avogadro        Avogadro's number (N) in particles/mole
    lightspd        speed of light in vacuum (c) in cm/ps
    boltzmann       Boltzmann constant (kB) in g*Ang**2/ps**2/mole/K
    gasconst        ideal gas constant (R) in kcal/mole/K
    elemchg         elementary charge of a proton in Coulombs
    vacperm         vacuum permittivity (electric constant, eps0) in F/m
    emass           mass of an electron in atomic mass units
    planck          Planck's constant (h) in J-s
    joule           conversion from calorie to joule
    ekcal           conversion from kcal to g*Ang**2/ps**2
    bohr            conversion from Bohr to Angstrom
    hartree         conversion from Hartree to kcal/mole
    evolt           conversion from Hartree to electron-volt
    efreq           conversion from Hartree to cm-1
    coulomb         conversion from electron**2/Ang to kcal/mole
    elefield        conversion from electron**2/Ang to megavolt/cm
    debye           conversion from electron-Ang to Debye
    prescon         conversion from kcal/mole/Ang**3 to Atm

UPRIOR Module previous values of induced dipoles

    maxpred         maximum number of predictor induced dipoles to save
    nualt           number of sets of prior induced dipoles in storage
    maxualt         number of sets of induced dipoles needed for predictor
    gear            coefficients for Gear predictor binomial method
    aspc            coefficients for always stable predictor-corrector
    bpred           coefficients for induced dipole predictor polynomial
    bpredp          coefficients for predictor polynomial in energy field
    bpreds          coefficients for predictor for PB/GK solvation
    bpredps         coefficients for predictor in PB/GK energy field
    udalt           prior values for induced dipoles at each site
    upalt           prior values for induced dipoles in energy field
    usalt           prior values for induced dipoles for PB/GK solvation
    upsalt          prior values for induced dipoles in PB/GK energy field
    use_pred        flag to control use of induced dipole prediction
    polpred         type of predictor polynomial (GEAR, ASPC or LSQR)

UREY Module Urey-Bradley interactions in structure

    nurey           total number of Urey-Bradley terms in the system
    iury            numbers of the atoms in each Urey-Bradley interaction
    uk              Urey-Bradley force constants (kcal/mole/Ang**2)
    ul              ideal 1-3 distance values in Angstroms

URYPOT Module Urey-Bradley functional form details

    cury            cubic coefficient in Urey-Bradley potential
    qury            quartic coefficient in Urey-Bradley potential
    ureyunit        convert Urey-Bradley energy to kcal/mole

USAGE Module atoms active during energy computation

    nuse            total number of active atoms in energy calculation
    iuse            numbers of the atoms active in energy calculation
    use             true if an atom is active, false if inactive

VALFIT Module valence term parameter fitting values

    fit_bond        logical flag to fit bond stretch parameters
    fit_angle       logical flag to fit angle bend parameters
    fit_strbnd      logical flag to fit stretch-bend parameters
    fit_urey        logical flag to fit Urey-Bradley parameters
    fit_opbend      logical flag to fit out-of-plane bend parameters
    fit_tors        logical flag to fit torsional parameters
    fit_struct      logical flag to structure-fit valence parameters
    fit_force       logical flag to force-fit valence parameters

VDW Module van der Waals terms in current structure

    nvdw            total number van der Waals sites in the system
    ivdw            number of the atom for each van der Waals site
    jvdw            index into the vdw parameter matrix for each atom
    mvdw            index into the vdw parameter matrix for each class
    ired            attached atom from which reduction factor is applied
    kred            value of reduction factor parameter for each atom
    xred            reduced x-coordinate for each atom in the system
    yred            reduced y-coordinate for each atom in the system
    zred            reduced z-coordinate for each atom in the system
    radmin          minimum energy distance for each atom class pair
    epsilon         well depth parameter for each atom class pair
    radmin4         minimum energy distance for 1-4 interaction pairs
    epsilon4        well depth parameter for 1-4 interaction pairs
    radhbnd         minimum energy distance for hydrogen bonding pairs
    epshbnd         well depth parameter for hydrogen bonding pairs

VDWPOT Module van der Waals functional form details

    igauss          coefficients of Gaussian fit to vdw potential
    ngauss          number of Gaussians used in fit to vdw potential
    abuck           value of "A" constant in Buckingham vdw potential
    bbuck           value of "B" constant in Buckingham vdw potential
    cbuck           value of "C" constant in Buckingham vdw potential
    ghal            value of "gamma" in buffered 14-7 vdw potential
    dhal            value of "delta" in buffered 14-7 vdw potential
    v2scale         factor by which 1-2 vdw interactions are scaled
    v3scale         factor by which 1-3 vdw interactions are scaled
    v4scale         factor by which 1-4 vdw interactions are scaled
    v5scale         factor by which 1-5 vdw interactions are scaled
    use_vcorr       flag to use long range van der Waals correction
    vdwindex        indexing mode (atom type or class) for vdw parameters
    vdwtyp          type of van der Waals potential energy function
    radtyp          type of parameter (sigma or R-min) for atomic size
    radsiz          atomic size provided as radius or diameter
    radrule         combining rule for atomic size parameters
    epsrule         combining rule for vdw well depth parameters
    gausstyp        type of Gaussian fit to van der Waals potential

VIBS Module iterative vibrational analysis components

    rho             trial vectors for iterative vibrational analysis
    rhok            alternate vectors for iterative vibrational analysis
    rwork           temporary work array for eigenvector transformation

VIRIAL Module components of internal virial tensor

    vir             total internal virial Cartesian tensor components
    use_virial      logical flag governing use of virial computation

WARP Module potential surface smoothing parameters

    deform          value of the smoothing deformation parameter
    difft           diffusion coefficient for torsional potential
    diffv           diffusion coefficient for van der Waals potential
    diffc           diffusion coefficient for charge-charge potential
    m2              second moment of the GDA gaussian for each atom
    use_smooth      flag to use a potential energy smoothing method
    use_dem         flag to use diffusion equation method potential
    use_gda         flag to use gaussian density annealing potential
    use_tophat      flag to use analytical tophat smoothed potential
    use_stophat     flag to use shifted tophat smoothed potential

XTALS Module structures used for parameter fitting

    maxlsq          maximum number of least squares variables
    maxrsd          maximum number of residual functions
    nxtal           number of molecular structures to be stored
    nvary           number of potential parameters to optimize
    ivary           index for the types of potential parameters
    iresid          structure to which each residual function refers
    vary            atom numbers involved in potential parameters
    e0_lattice      ideal lattice energy for the current crystal
    varxtl          type of each potential parameter to be optimized
    rsdxtl          experimental variable for each of the residuals

ZCLOSE Module Z-matrix ring openings and closures

    nadd            number of added bonds between Z-matrix atoms
    ndel            number of bonds between Z-matrix bonds to delete
    iadd            numbers of the atom pairs defining added bonds
    idel            numbers of the atom pairs defining deleted bonds

ZCOORD Module Z-matrix internal coordinate values

    iz              defining atom numbers for each Z-matrix atom
    zbond           bond length used to define each Z-matrix atom
    zang            bond angle used to define each Z-matrix atom
    ztors           angle or torsion used to define Z-matrix atom