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** .. code-block:: text 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 **ALIGN Module        information for structure superposition** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text 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 valence 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 story descriptive type for each atom in system **ATOMS Module        number, position and type of atoms** .. code-block:: text 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** .. code-block:: text 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 anisotrop logical flag governing use of anisotropic pressure thermostat choice of temperature control method to be used barostat choice of pressure control method to be used volscale choice of scaling method for Monte Carlo barostat **BITOR Module        bitorsions in the current structure** .. code-block:: text nbitor total number of bitorsions in the system ibitor numbers of the atoms in each bitorsion **BNDPOT Module        bond stretch functional form details** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text 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 **BOXES Module        periodic boundary condition parameters** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text ctrntyp type of charge transfer term (SEPARATE or COMBINED) **DERIV Module        Cartesian coord derivative components** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text exfld components of applied external electric field use_exfld flag to include applied external electric field **FACES Module        Connolly area and volume variables** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text nrat number of holonomic distance constraints to apply nratx number of atom group holonomic constraints to apply iratx group number of group in a holonomic constraint kratx spatial constraint type (1=plane, 2=line, 3=point) irat atom numbers of atoms in a holonomic constraint rateps convergence tolerance for holonomic constraints krat ideal distance value for holonomic constraint use_rattle logical flag to set use of holonomic contraints ratimage flag to use minimum image for holonomic constraint **GKSTUF Module        generalized Kirkwood solvation values** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text hesscut magnitude of smallest allowed Hessian element **HESSN Module        Cartesian Hessian elements for one atom** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text nfree_aux total degrees of freedom for auxiliary dipoles tautemp_aux time constant for auliliary 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** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text einter total intermolecular potential energy **IOUNIT Module        Fortran input/output unit numbers** .. code-block:: text 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** .. code-block:: text anan angle-angle cross term parameters for each atom class **KANGS Module        bond angle bend forcefield parameters** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text chg partial charge parameters for each atom type **KCPEN Module        charge penetration forcefield parameters** .. code-block:: text cpele valence electron magnitude for each atom class cpalp alpha charge penetration parameter for each atom class **KCTRN Module        charge transfer forcefield parameters** .. code-block:: text ctchg charge transfer magnitude for each atom class ctdmp alpha charge transfer parameter for each atom class **KDIPOL Module        bond dipole forcefield parameters** .. code-block:: text 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** .. code-block:: text dspsix C6 dispersion coefficient for each atom class dspdmp alpha dispersion parameter for each atom class **KEXPL Module        exch-polarization forcefield parameters** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text 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 **KSTBND Module        stretch-bend forcefield parameters** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text rad van der Waals radius parameter for each atom type eps van der Waals well depth parameter for each atom type 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 type **LIGHT Module        method of lights pair neighbors indices** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text 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 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 rcav atomic radius of each atom for cavitation energy rdisp atomic radius of each atom for dispersion energy cdisp maximum dispersion energy for each atom **NUCLEO Module        parameters for nucleic acid structure** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text nproc number of processors available to OpenMP nthread number of threads to be used with OpenMP **ORBITS Module        conjugated pisystem orbital energies** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text 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. .. code-block:: text 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** .. code-block:: text npdb number of atoms stored in Protein Data Bank format nres number of residues stored in Protein Data Bank format 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 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 pdbres Protein Data Bank residue name assigned to each atom pdbatm Protein Data Bank atom name assigned to each atom pdbtyp 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** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text 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 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** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text 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 seq three-letter code for each residue in the sequence chnnam one-letter identifier for each sequence chain chntyp contents of each chain (GENERIC, PEPTIDE or NUCLEIC) **SHUNT Module        polynomial switching function values** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text 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 **SOLUTE Module        continuum solvation model parameters** .. code-block:: text doffset dielectric offset to continuum solvation atomic radii 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 rsolv atomic radius of each atom for continuum solvation 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 solvtyp type of continuum solvation energy model in use borntyp method to be used for the Born radius computation **STODYN Module        SD trajectory frictional coefficients** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text ntpair number of stored dipole-dipole matrix elements tindex index into stored dipole-dipole matrix values tdipdip stored dipole-dipole matrix element values **TITLES Module        title for current molecular system** .. code-block:: text ltitle length in characters of the nonblank title string title title used to describe the current structure **TORPOT Module        torsional functional form details** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text ntortor total number of torsion-torsion interactions itt atoms and parameter indices for torsion-torsion **TREE Module        potential smoothing search tree levels** .. code-block:: text 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 **UNITS Module        physical constants and unit conversions** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text vir total internal virial Cartesian tensor components use_virial logical flag governing use of virial computation **WARP Module        potential surface smoothing parameters** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text 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** .. code-block:: text 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