Modules & Global Variables

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

ACTION Module        total number of each energy term type

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

ALIGN Module        information for structure superposition

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

ANALYZ Module        energy components partitioned to atoms

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

ANGANG Module        angle-angles in current structure

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

ANGBND Module        bond angle bends in current structure

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

ANGPOT Module        angle bend functional form details

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

ANGTOR Module        angle-torsions in current structure

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

ARGUE Module        command line arguments at run time

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

ASCII Module        selected ASCII character code values

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

ATMLST Module        bond and angle local geometry indices

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

ATOMID Module        atomic properties for current atoms

tag             integer atom labels from input coordinates file
class           atom class number for each atom in the system
atomic          atomic number for each atom in the system
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

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

BATH Module        thermostat and barostat control values

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

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

BNDPOT Module        bond stretch functional form details

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

BNDSTR Module        bond stretches in the current structure

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

BOUND Module        periodic boundary condition controls

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

BOXES Module        periodic boundary condition parameters

xbox            length of a-axis of periodic box in Angstroms
ybox            length of b-axis of periodic box in Angstroms
zbox            length of c-axis of periodic box in Angstroms
alpha           angle between b- and c-axes of box in degrees
beta            angle between a- and c-axes of box in degrees
gamma           angle between a- and b-axes of box in degrees
xbox2           half of the a-axis length of periodic box
ybox2           half of the b-axis length of periodic box
zbox2           half of the c-axis length of periodic box
box34           three-fourths axis length of truncated octahedron
volbox          volume in Ang**3 of the periodic box
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
spacegrp        space group symbol for the unit cell type

CELL Module        replicated cell periodic boundaries

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

CFLUX Module        charge flux terms in current system

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

CHARGE Module        partial charges in current structure

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

CHGPEN Module        charge penetration in current structure

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

CHGPOT Module        charge-charge functional form details

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

CHGTRN Module        charge transfer for current structure

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

CHRONO Module        clock time values for current program

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

CHUNKS Module        PME grid spatial decomposition values

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

COUPLE Module        atom neighbor connectivity lists

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

CTRPOT Module        charge transfer functional form details

ctrntyp         type of charge transfer term (SEPARATE or COMBINED)

DERIV Module        Cartesian coord derivative components

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

DIPOLE Module        bond dipoles in current structure

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

DISGEO Module        distance geometry bounds & parameters

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

DISP Module        damped dispersion for current structure

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

DMA Module        QM spherical harmonic multipole moments

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

DOMEGA Module        derivative components over torsions

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

DSPPOT Module        dispersion interaction scale factors

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

ENERGI Module        individual potential energy components

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

EWALD Module        Ewald summation parameters and options

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

FACES Module        Connolly area and volume variables

maxcls          maximum number of neighboring atom pairs
maxtt           maximum number of temporary tori
maxt            maximum number of total tori
maxp            maximum number of probe positions
maxv            maximum number of vertices
maxen           maximum number of concave edges
maxfn           maximum number of concave faces
maxc            maximum number of circles
maxeq           maximum number of convex edges
maxfs           maximum number of saddle faces
maxfq           maximum number of convex faces
maxcy           maximum number of cycles
mxcyeq          maximum number of convex edge cycles
mxfqcy          maximum number of convex face cycles

FFT Module        Fast Fourier transform control values

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

FIELDS Module        molecular mechanics force field type

maxbio          maximum number of biopolymer atom definitions
biotyp          force field atom type of each biopolymer type
forcefield      string used to describe the current forcefield

FILES Module        name & number of current structure file

nprior          number of previously existing cycle files
ldir            length in characters of the directory name
leng            length in characters of the base filename
filename        base filename used by default for all files
outfile         output filename used for intermediate results

FRACS Module        distances to molecular center of mass

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

FREEZE Module        definition of holonomic constraints

nrat            number of holonomic distance constraints to apply
nratx           number of atom group holonomic constraints to apply
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

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

GROUP Module        partitioning of system into atom groups

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

HESCUT Module        cutoff for Hessian matrix elements

hesscut         magnitude of smallest allowed Hessian element

HESSN Module        Cartesian Hessian elements for one atom

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

HPMF Module        hydrophobic potential of mean force term

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

IELSCF Module        extended Lagrangian induced dipoles

nfree_aux       total degrees of freedom for auxiliary dipoles
tautemp_aux     time constant for 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

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

IMPTOR Module        improper torsions in current structure

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

INFORM Module        program I/O and flow control values

maxask          maximum number of queries for interactive input
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)
silent          logical flag to turn off all information printing
verbose         logical flag to turn on extra information printing
debug           logical flag to turn on full debug printing
holdup          logical flag to wait for carriage return on exit
abort           logical flag to stop execution at next chance

INTER Module        sum of intermolecular energy components

einter          total intermolecular potential energy

IOUNIT Module        Fortran input/output unit numbers

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

KANANG Module        angle-angle term forcefield parameters

anan            angle-angle cross term parameters for each atom class

KANGS Module        bond angle bend forcefield parameters

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

KANTOR Module        angle-torsion forcefield parameters

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

KATOMS Module        atom definition forcefield parameters

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

KBONDS Module        bond stretching forcefield parameters

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

KCHRGE Module        partial charge forcefield parameters

chg             partial charge parameters for each atom type

KCPEN Module        charge penetration forcefield parameters

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

KCTRN Module        charge transfer forcefield parameters

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

KDIPOL Module        bond dipole forcefield parameters

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

KDSP Module        damped dispersion forcefield parameters

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

KEYS Module        contents of the keyword control file

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

KHBOND Module        H-bonding term forcefield parameters

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

KIPROP Module        improper dihedral forcefield parameters

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

KITORS Module        improper torsion forcefield parameters

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

KMULTI Module        atomic multipole forcefield parameters

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

KOPBND Module        out-of-plane bend forcefield parameters

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

KOPDST Module        out-of-plane distance forcefield params

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

KORBS Module        pisystem orbital forcefield parameters

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

KPITOR Module        pi-system torsion forcefield parameters

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

KPOLR Module        polarizability forcefield parameters

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

KREPL Module        Pauli repulsion forcefield parameters

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

KSTBND Module        stretch-bend forcefield parameters

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

KSTTOR Module        stretch-torsion forcefield parameters

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

KTORSN Module        torsional angle forcefield parameters

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

KTRTOR Module        torsion-torsion forcefield parameters

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

KURYBR Module        Urey-Bradley term forcefield parameters

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

KVDWPR Module        special vdw term forcefield parameters

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

KVDWS Module        van der Waals term forcefield parameters

rad             van der Waals radius parameter for each atom 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

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

LIMITS Module        interaction taper & cutoff distances

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

LINMIN Module        line search minimization parameters

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
intmax          maximum number of interpolations during line search

MATH Module        mathematical and geometrical constants

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

MDSTUF Module        molecular dynamics trajectory controls

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

MERCK Module        MMFF-specific force field parameters

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

MINIMA Module        general parameters for minimizations

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

MOLCUL Module        individual molecules in current system

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

MOLDYN Module        MD trajectory velocity & acceleration

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

MOMENT Module        electric multipole moment components

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

MPLPOT Module        multipole functional form details

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

MPOLE Module        atomic multipoles in current structure

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

MRECIP Module        reciprocal PME for permanent multipoles

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

MUTANT Module        free energy calculation hybrid atoms

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

NEIGH Module        pairwise neighbor list indices & storage

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

NONPOL Module        nonpolar cavity & dispersion parameters

epso            water oxygen eps for implicit dispersion term
epsh            water hydrogen eps for implicit dispersion term
rmino           water oxygen Rmin for implicit dispersion term
rminh           water hydrogen Rmin for implicit dispersion term
awater          water number density at standard temp & pressure
slevy           enthalpy-to-free energy scale factor for dispersion
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

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

OMEGA Module        torsional space dihedral angle values

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

OPBEND Module        out-of-plane bends in current structure

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

OPDIST Module        out-of-plane distances in structure

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

OPENMP Module        OpenMP processor and thread values

nproc           number of processors available to OpenMP
nthread         number of threads to be used with OpenMP

ORBITS Module        conjugated pisystem orbital energies

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

OUTPUT Module        output file format control parameters

archive         logical flag to save structures in an archive
noversion       logical flag governing use of filename versions
overwrite       logical flag to overwrite intermediate files inplace
cyclesave       logical flag to mark use of numbered cycle files
velsave         logical flag to save velocity vector components
frcsave         logical flag to save force vector components
uindsave        logical flag to save induced atomic dipoles
coordtype       selects Cartesian, internal, rigid body or none

PARAMS Module        force field parameter file contents

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

PATHS Module        Elber reaction path method parameters

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

PBSTUF Module        Poisson-Boltzmann solvation parameters

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

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

PDB Module        Protein Data Bank structure definition

npdb            number of atoms stored in Protein Data Bank format
nres            number of residues stored in Protein Data Bank format
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

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

PIORBS Module        conjugated system in current structure

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

PISTUF Module        bond order-related pisystem parameters

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

PITORS Module        pi-system torsions in current structure

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

PME Module        values for particle mesh Ewald summation

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

POLAR Module        induced dipole moments & polarizability

npolar          total number of polarizable sites in the system
ipolar          number of the multipole for each polarizable site
polarity        dipole polarizability for each multipole site (Ang**3)
thole           Thole polarizability damping value for each site
dirdamp         direct polarization damping value for each site
pdamp           value of polarizability scale factor for each site
udir            direct induced dipole components at each multipole site
udirp           direct induced dipoles in field used for energy terms
udirs           direct GK or PB induced dipoles at each multipole site
udirps          direct induced dipoles in field used for GK or PB energy
uind            mutual induced dipole components at each multipole site
uinp            mutual induced dipoles in field used for energy terms
uinds           mutual GK or PB induced dipoles at each multipole 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 atomic site

POLGRP Module        polarization group connectivity lists

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

POLOPT Module        induced dipoles for OPT extrapolation

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

POLPCG Module        induced dipoles via the PCG solver

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

POLPOT Module        polarization functional form details

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

POLTCG Module        induced dipoles via the TCG solver

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

POTENT Module        usage of potential energy components

use_bond        logical flag governing use of bond stretch potential
use_angle       logical flag governing use of angle bend potential
use_strbnd      logical flag governing use of stretch-bend potential
use_urey        logical flag governing use of Urey-Bradley potential
use_angang      logical flag governing use of angle-angle cross term
use_opbend      logical flag governing use of out-of-plane bend term
use_opdist      logical flag governing use of out-of-plane distance
use_improp      logical flag governing use of improper dihedral term
use_imptor      logical flag governing use of improper torsion term
use_tors        logical flag governing use of torsional potential
use_pitors      logical flag governing use of pi-system torsion term
use_strtor      logical flag governing use of stretch-torsion term
use_angtor      logical flag governing use of angle-torsion term
use_tortor      logical flag governing use of torsion-torsion term
use_vdw         logical flag governing use of vdw der Waals potential
use_repuls      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

POTFIT Module        values for electrostatic potential fit

nconf           total number of configurations to be analyzed
namax           maximum number of atoms in the largest configuration
ngatm           total number of atoms with active potential grid points
nfatm           total number of atoms in electrostatic potential fit
npgrid          total number of electrostatic potential grid points
ipgrid          atom associated with each potential grid point
resp            weight used to restrain parameters to original values
xdpl0           target x-component of the molecular dipole moment
ydpl0           target y-component of the molecular dipole moment
zdpl0           target z-component of the molecular dipole moment
xxqdp0          target xx-component of the molecular quadrupole moment
xyqdp0          target xy-component of the molecular quadrupole moment
xzqdp0          target xz-component of the molecular quadrupole moment
yyqdp0          target yy-component of the molecular quadrupole moment
yzqdp0          target yz-component of the molecular quadrupole moment
zzqdp0          target zz-component of the 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
fitchg          flag marking atom types for use in partial charge fit
fitpol          flag marking atom types for use in atomic multipole fit
gatm            flag to use potential grid points around each atom
fatm            flag to use each atom in electrostatic potential fit

PTABLE Module        symbols and info for chemical elements

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

REFER Module        reference atomic coordinate storage

nref            total number of atoms in each reference system
refltitle       length in characters of each reference title line
refleng         length in characters of each reference filename
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         base filename for each reference system
reftitle        title used to describe each reference system

REPEL Module        Pauli repulsion for current structure

nrep            total number of repulsion sites in the system
sizpr           Pauli repulsion size parameter value at each site
dmppr           Pauli repulsion alpha damping value at each site
elepr           Pauli repulsion valence electrons at each site

REPPOT Module        repulsion interaction scale factors

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

RESDUE Module        amino acid & nucleotide residue names

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

RESTRN Module        parameters for geometrical restraints

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

RGDDYN Module        rigid body MD velocities and momenta

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

RIGID Module        rigid body coordinates for atom groups

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

RING Module        number and location of ring structures

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

ROTBND Module        molecule partitions for bond rotation

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

RXNFLD Module        reaction field matrix and indices

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

RXNPOT Module        reaction field functional form details

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

SCALES Module        optimization parameter scale factors

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

SEQUEN Module        sequence information for biopolymer

nseq            total number of residues in biopolymer sequences
nchain          number of separate biopolymer sequence chains
ichain          first and last residue in each biopolymer chain
seqtyp          residue type for each residue in the sequence
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

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

“sizes” sets values for critical array dimensions used throughout the software; these parameters fix the size of the largest systems that can be handled

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

SOCKET Module        socket communication control parameters

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

SOLUTE Module        continuum solvation model parameters

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

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

STRBND Module        stretch-bends in current structure

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

STRTOR Module        stretch-torsions in current structure

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

SYNTRN Module        synchronous transit path definition

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

TARRAY Module        store dipole-dipole matrix elements

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

TITLES Module        title for current molecular system

ltitle          length in characters of the nonblank title string
title           title used to describe the current structure

TORPOT Module        torsional functional form details

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

TORS Module        torsional angles in current structure

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

TORTOR Module        torsion-torsions in current structure

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

TREE Module        potential smoothing search tree levels

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

UNITS Module        physical constants and unit conversions

D. B. Newell, F. Cabiati, J. Fischer, K. Fujii, S. G. Karshenboim, S. Margolis, E. de Mirandes, P. J. Mohr, F. Nez, K. Pachucki, T. J. Quinn, N. Taylor, M. Wang, B. M. Wood and Z. Zhang, “The CODATA 2017 Values of h, e, k, and Na for the Revision of the SI”, Metrologia, 55, L13-L16 (2018)

P. J. Mohr, D. B. Newell and B. N. Taylor, “CODATA Recommended Values of the Fundamental Physical Constants: 2014”, Journal of Physical and Chemical Reference Data, 45, 043102 (2016)

Where available, values are from the 2017 CODATA adjustment based on exact physical constants for the revised SI

Other values are from the 2014 CODATA reference constants; also available online from the National Institute of Standards and Technology at http://physics.nist.gov/cuu/Constants/index.html/

The conversion from calorie to Joule is the definition of the thermochemical calorie as 1 cal = 4.1840 J from ISO 31-4 (1992)

The “coulomb” energy conversion factor is found by dimensional analysis of Coulomb’s Law, ie, by dividing the square of the elementary charge in Coulombs by 4*pi*eps0*rij, where eps0 is the permittivity of vacuum (the “electric constant”); note that eps0 is typically given in F/m, equivalent to C**2/(J-m)

The approximate value used for the Debye, 3.33564 x 10-30 C-m, is from IUPAC Compendium of Chemical Technology, 2nd Ed. (1997)

The value of “prescon” is based on definition of 1 atmosphere as 101325 Pa set by the 10th Conference Generale des Poids et Mesures (1954), where a Pascal (Pa) is equal to a J/m**3

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
debye           conversion from electron-Ang to Debye
prescon         conversion from kcal/mole/Ang**3 to Atm

UPRIOR Module        previous values of induced dipoles

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

UREY Module        Urey-Bradley interactions in structure

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

URYPOT Module        Urey-Bradley functional form details

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

USAGE Module        atoms active during energy computation

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

VALFIT Module        valence term parameter fitting values

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

VDW Module        van der Waals terms in current structure

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

VDWPOT Module        van der Waals functional form details

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

VIBS Module        iterative vibrational analysis components

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

VIRIAL Module        components of internal virial tensor

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

WARP Module        potential surface smoothing parameters

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

XTALS Module        structures used for parameter fitting

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

ZCLOSE Module        Z-matrix ring openings and closures

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

ZCOORD Module        Z-matrix internal coordinate values

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