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
alpha_sin sine of the alpha periodic box angle
alpha_cos cosine of the alpha periodic box angle
beta_sin sine of the beta periodic box angle
beta_cos cosine of the beta periodic box angle
gamma_sin sine of the gamma periodic box angle
gamma_cos cosine of the gamma periodic box angle
beta_term term used in generating triclinic box
gamma_term term used in generating triclinic box
lvec real space lattice vectors as matrix rows
recip reciprocal lattice vectors as matrix columns
orthogonal flag to mark periodic box as orthogonal
monoclinic flag to mark periodic box as monoclinic
triclinic flag to mark periodic box as triclinic
octahedron flag to mark box as truncated octahedron
dodecadron flag to mark box as rhombic dodecahedron
nonprism flag to mark octahedron or dodecahedron
nosymm flag to mark use or lack of lattice symmetry
spacegrp space group symbol for the unit cell type
CELL Module replicated cell periodic boundaries
ncell total number of cell replicates for periodic boundaries
icell offset along axes for each replicate periodic cell
xcell length of the a-axis of the complete replicated cell
ycell length of the b-axis of the complete replicated cell
zcell length of the c-axis of the complete replicated cell
xcell2 half the length of the a-axis of the replicated cell
ycell2 half the length of the b-axis of the replicated cell
zcell2 half the length of the c-axis of the replicated cell
CFLUX Module charge flux terms in current system
bflx bond stretching charge flux constant (electrons/Ang)
aflx angle bending charge flux constant (electrons/radian)
abflx asymmetric stretch charge flux constant (electrons/Ang)
CHARGE Module partial charges in current structure
nion total number of partial charges in system
iion number of the atom site for each partial charge
jion neighbor generation site for each partial charge
kion cutoff switching site for each partial charge
pchg current atomic partial charge values (e-)
pchg0 original partial charge values for charge flux
CHGPEN Module charge penetration in current structure
ncp total number of charge penetration sites in system
pcore number of core electrons at each multipole site
pval number of valence electrons at each multipole site
pval0 original number of valence electrons for charge flux
palpha charge penetration damping at each multipole site
CHGPOT Module charge-charge functional form details
electric energy factor in kcal/mole for current force field
dielec dielectric constant for electrostatic interactions
ebuffer electrostatic buffering constant added to distance
c1scale factor by which 1-1 charge interactions are scaled
c2scale factor by which 1-2 charge interactions are scaled
c3scale factor by which 1-3 charge interactions are scaled
c4scale factor by which 1-4 charge interactions are scaled
c5scale factor by which 1-5 charge interactions are scaled
neutnbr logical flag governing use of neutral group neighbors
neutcut logical flag governing use of neutral group cutoffs
CHGTRN Module charge transfer for current structure
nct total number of dispersion sites in the system
chgct charge for charge transfer at each multipole site
dmpct charge transfer damping factor at each multipole site
CHRONO Module clock time values for current program
twall current processor wall clock time in seconds
tcpu elapsed cpu time from start of program in seconds
CHUNKS Module PME grid spatial decomposition values
nchunk total number of spatial regions for PME grid
nchk1 number of spatial regions along the a-axis
nchk2 number of spatial regions along the b-axis
nchk3 number of spatial regions along the c-axis
ngrd1 number of grid points per region along a-axis
ngrd2 number of grid points per region along b-axis
ngrd3 number of grid points per region along c-axis
nlpts PME grid points to the left of center point
nrpts PME grid points to the right of center point
grdoff offset for index into B-spline coefficients
pmetable PME grid spatial regions involved for each site
COUPLE Module atom neighbor connectivity lists
n12 number of atoms directly bonded to each atom
n13 number of atoms in a 1-3 relation to each atom
n14 number of atoms in a 1-4 relation to each atom
n15 number of atoms in a 1-5 relation to each atom
i12 atom numbers of atoms 1-2 connected to each atom
i13 atom numbers of atoms 1-3 connected to each atom
i14 atom numbers of atoms 1-4 connected to each atom
i15 atom numbers of atoms 1-5 connected to each atom
CTRPOT Module charge transfer functional form details
ctrntyp type of charge transfer term (SEPARATE or COMBINED)
DERIV Module Cartesian coord derivative components
desum total energy Cartesian coordinate derivatives
deb bond stretch Cartesian coordinate derivatives
dea angle bend Cartesian coordinate derivatives
deba stretch-bend Cartesian coordinate derivatives
deub Urey-Bradley Cartesian coordinate derivatives
deaa angle-angle Cartesian coordinate derivatives
deopb out-of-plane bend Cartesian coordinate derivatives
deopd out-of-plane distance Cartesian coordinate derivatives
deid improper dihedral Cartesian coordinate derivatives
deit improper torsion Cartesian coordinate derivatives
det torsional Cartesian coordinate derivatives
dept pi-system torsion Cartesian coordinate derivatives
debt stretch-torsion Cartesian coordinate derivatives
deat angle-torsion Cartesian coordinate derivatives
dett torsion-torsion Cartesian coordinate derivatives
dev van der Waals Cartesian coordinate derivatives
der Pauli repulsion Cartesian coordinate derivatives
dedsp damped dispersion Cartesian coordinate derivatives
dec charge-charge Cartesian coordinate derivatives
decd charge-dipole Cartesian coordinate derivatives
ded dipole-dipole Cartesian coordinate derivatives
dem multipole Cartesian coordinate derivatives
dep polarization Cartesian coordinate derivatives
dect charge transfer Cartesian coordinate derivatives
derxf reaction field Cartesian coordinate derivatives
des solvation Cartesian coordinate derivatives
delf metal ligand field Cartesian coordinate derivatives
deg geometric restraint Cartesian coordinate derivatives
dex extra energy term Cartesian coordinate derivatives
DIPOLE Module bond dipoles in current structure
ndipole total number of dipoles in the system
idpl numbers of atoms that define each dipole
bdpl magnitude of each of the dipoles (Debye)
sdpl position of each dipole between defining atoms
DISGEO Module distance geometry bounds & parameters
vdwmax maximum value of hard sphere sum for an atom pair
compact index of local distance compaction on embedding
pathmax maximum value of upper bound after smoothing
dbnd distance geometry upper and lower bounds matrix
georad hard sphere radii for distance geometry atoms
use_invert flag to use enantiomer closest to input structure
use_anneal flag to use simulated annealing refinement
DISP Module damped dispersion for current structure
ndisp total number of dispersion sites in the system
idisp number of the atom for each dispersion site
csixpr pairwise sum of C6 dispersion coefficients
csix C6 dispersion coefficient value at each site
adisp alpha dispersion damping value at each site
DMA Module QM spherical harmonic multipole moments
mp atomic monopole charge values from DMA
dpx atomic dipole moment x-component from DMA
dpy atomic dipole moment y-component from DMA
dpz atomic dipole moment z-component from DMA
q20 atomic Q20 quadrupole component from DMA (zz)
q21c atomic Q21c quadrupole component from DMA (xz)
q21s atomic Q21s quadrupole component from DMA (yz)
q22c atomic Q22c quadrupole component from DMA (xx-yy)
q22s atomic Q22s quadrupole component from DMA (xy)
DOMEGA Module derivative components over torsions
tesum total energy derivatives over torsions
teb bond stretch derivatives over torsions
tea angle bend derivatives over torsions
teba stretch-bend derivatives over torsions
teub Urey-Bradley derivatives over torsions
teaa angle-angle derivatives over torsions
teopb out-of-plane bend derivatives over torsions
teopd out-of-plane distance derivatives over torsions
teid improper dihedral derivatives over torsions
teit improper torsion derivatives over torsions
tet torsional derivatives over torsions
tept pi-system torsion derivatives over torsions
tebt stretch-torsion derivatives over torsions
teat angle-torsion derivatives over torsions
tett torsion-torsion derivatives over torsions
tev van der Waals derivatives over torsions
ter Pauli repulsion derivatives over torsions
tedsp dampled dispersion derivatives over torsions
tec charge-charge derivatives over torsions
tecd charge-dipole derivatives over torsions
ted dipole-dipole derivatives over torsions
tem atomic multipole derivatives over torsions
tep polarization derivatives over torsions
tect charge transfer derivatives over torsions
terxf reaction field derivatives over torsions
tes solvation derivatives over torsions
telf metal ligand field derivatives over torsions
teg geometric restraint derivatives over torsions
tex extra energy term derivatives over torsions
DSPPOT Module dispersion interaction scale factors
dsp2scale scale factor for 1-2 dispersion energy interactions
dsp3scale scale factor for 1-3 dispersion energy interactions
dsp4scale scale factor for 1-4 dispersion energy interactions
dsp5scale scale factor for 1-5 dispersion energy interactions
use_dcorr flag to use long range dispersion correction
ENERGI Module individual potential energy components
esum total potential energy of the system
eb bond stretch potential energy of the system
ea angle bend potential energy of the system
eba stretch-bend potential energy of the system
eub Urey-Bradley potential energy of the system
eaa angle-angle potential energy of the system
eopb out-of-plane bend potential energy of the system
eopd out-of-plane distance potential energy of the system
eid improper dihedral potential energy of the system
eit improper torsion potential energy of the system
et torsional potential energy of the system
ept pi-system torsion potential energy of the system
ebt stretch-torsion potential energy of the system
eat angle-torsion potential energy of the system
ett torsion-torsion potential energy of the system
ev van der Waals potential energy of the system
er Pauli repulsion potential energy of the system
edsp dampled dispersion potential energy of the system
ec charge-charge potential energy of the system
ecd charge-dipole potential energy of the system
ed dipole-dipole potential energy of the system
em atomic multipole potential energy of the system
ep polarization potential energy of the system
ect charge transfer potential energy of the system
erxf reaction field potential energy of the system
es solvation potential energy of the system
elf metal ligand field potential energy of the system
eg geometric restraint potential energy of the system
ex extra term potential energy of the system
EWALD Module Ewald summation parameters and options
aewald current value of Ewald convergence coefficient
aeewald Ewald convergence coefficient for electrostatics
apewald Ewald convergence coefficient for polarization
adewald Ewald convergence coefficient for dispersion
boundary Ewald boundary condition; none, tinfoil or vacuum
EXPOL Module exch-polarization in current structure
nexpol total number of exch polarization sites in system
kpep exchange polarization spring constant at each site
prepep exchange polarization prefactor at each site
dmppep exchange polarization damping alpha at each site
polscale scale matrix for use in exchange polarization
polinv scale matrix inverse for exchange polarization
lpep flag to use exchange polarization at each site
EXTFLD Module applied external electric field vector
exfld components of applied external electric field
use_exfld flag to include applied external electric field
FACES Module Connolly area and volume variables
maxcls maximum number of neighboring atom pairs
maxtt maximum number of temporary tori
maxt maximum number of total tori
maxp maximum number of probe positions
maxv maximum number of vertices
maxen maximum number of concave edges
maxfn maximum number of concave faces
maxc maximum number of circles
maxeq maximum number of convex edges
maxfs maximum number of saddle faces
maxfq maximum number of convex faces
maxcy maximum number of cycles
mxcyeq maximum number of convex edge cycles
mxfqcy maximum number of convex face cycles
na number of atoms
pr probe radius
ar atomic radii
axyz atomic coordinates
skip if true, atom is not used
nosurf if true, atom has no free surface
afree atom free of neighbors
abur atom buried
cls atom numbers of neighbors
clst pointer from neighbor to torus
acls begin and end pointers for atoms neighbors
ntt number of temporary tori
ttfe first edge of each temporary torus
ttle last edge of each temporary torus
enext pointer to next edge of temporary torus
tta temporary torus atom numbers
ttbur temporary torus buried
ttfree temporary torus free
nt number of tori
tfe torus first edge
ta torus atom numbers
tr torus radius
t torus center
tax torus axis
tfree torus free of neighbors
np number of probe positions
pa probe position atom numbers
p probe position coordinates
nv number of vertices
va vertex atom number
vp vertex probe number
vxyz vertex coordinates
nen number of concave edges
nfn number of concave faces
env vertex numbers for each concave edge
fnen concave face concave edge numbers
nc number of circles
ca circle atom number
ct circle torus number
cr circle radius
c circle center
neq number of convex edges
eqc convex edge circle number
eqv convex edge vertex numbers
afe first convex edge of each atom
ale last convex edge of each atom
eqnext pointer to next convex edge of atom
nfs number of saddle faces
fsen saddle face concave edge numbers
fseq saddle face convex edge numbers
ncy number of cycles
cyneq number of convex edges in cycle
cyeq cycle convex edge numbers
nfq number of convex faces
fqa atom number of convex face
fqncy number of cycles bounding convex face
fqcy convex face cycle numbers
FFT Module Fast Fourier transform control values
maxprime maximum number of prime factors of FFT dimension
iprime prime factorization of each FFT dimension (FFTPACK)
planf pointer to forward transform data structure (FFTW)
planb pointer to backward transform data structure (FFTW)
ffttable intermediate array used by the FFT routine (FFTPACK)
ffttyp type of FFT package; currently FFTPACK or FFTW
FIELDS Module molecular mechanics force field type
biotyp force field atom type of each biopolymer type
forcefield string used to describe the current forcefield
FILES Module name & number of current structure file
nprior number of previously existing cycle files
ldir length in characters of the directory name
leng length in characters of the base filename
filename fill filename including any extension or version
outfile output filename used for intermediate results
FRACS Module distances to molecular center of mass
xfrac fractional coordinate along a-axis of center of mass
yfrac fractional coordinate along b-axis of center of mass
zfrac fractional coordinate along c-axis of center of mass
FREEZE Module definition of holonomic constraints
nrat number of holonomic distance constraints to apply
nratx number of atom group holonomic constraints to apply
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
gpucard integer flag for GPU use (0=no GPU, 1=GPU present)
digits decimal places output for energy and coordinates
iprint steps between status printing (0=no printing)
iwrite steps between coordinate saves (0=no saves)
isend steps between socket communication (0=no sockets)
verbose logical flag to turn on extra information printing
debug logical flag to turn on extensive debug printing
silent logical flag to turn off all information printing
holdup logical flag to wait for carriage return on exit
abort logical flag to stop execution at next chance
INTER Module sum of intermolecular energy components
einter total intermolecular potential energy
IOUNIT Module Fortran input/output unit numbers
input Fortran I/O unit for main input (default=5)
iout Fortran I/O unit for main output (default=6)
KANANG Module angle-angle term forcefield parameters
anan angle-angle cross term parameters for each atom class
KANGS Module bond angle bend forcefield parameters
maxna maximum number of harmonic angle bend parameter entries
maxna5 maximum number of 5-membered ring angle bend entries
maxna4 maximum number of 4-membered ring angle bend entries
maxna3 maximum number of 3-membered ring angle bend entries
maxnap maximum number of in-plane angle bend parameter entries
maxnaf maximum number of Fourier angle bend parameter entries
acon force constant parameters for harmonic angle bends
acon5 force constant parameters for 5-ring angle bends
acon4 force constant parameters for 4-ring angle bends
acon3 force constant parameters for 3-ring angle bends
aconp force constant parameters for in-plane angle bends
aconf force constant parameters for Fourier angle bends
ang bond angle parameters for harmonic angle bends
ang5 bond angle parameters for 5-ring angle bends
ang4 bond angle parameters for 4-ring angle bends
ang3 bond angle parameters for 3-ring angle bends
angp bond angle parameters for in-plane angle bends
angf phase shift angle and periodicity for Fourier bends
ka string of atom classes for harmonic angle bends
ka5 string of atom classes for 5-ring angle bends
ka4 string of atom classes for 4-ring angle bends
ka3 string of atom classes for 3-ring angle bends
kap string of atom classes for in-plane angle bends
kaf string of atom classes for Fourier angle bends
KANTOR Module angle-torsion forcefield parameters
maxnat maximum number of angle-torsion parameter entries
atcon torsional amplitude parameters for angle-torsion
kat string of atom classes for angle-torsion terms
KATOMS Module atom definition forcefield parameters
atmcls atom class number for each of the atom types
atmnum atomic number for each of the atom types
ligand number of atoms to be attached to each atom type
weight average atomic mass of each atom type
symbol modified atomic symbol for each atom type
describe string identifying each of the atom types
KBONDS Module bond stretching forcefield parameters
maxnb maximum number of bond stretch parameter entries
maxnb5 maximum number of 5-membered ring bond stretch entries
maxnb4 maximum number of 4-membered ring bond stretch entries
maxnb3 maximum number of 3-membered ring bond stretch entries
maxnel maximum number of electronegativity bond corrections
bcon force constant parameters for harmonic bond stretch
bcon5 force constant parameters for 5-ring bond stretch
bcon4 force constant parameters for 4-ring bond stretch
bcon3 force constant parameters for 3-ring bond stretch
blen bond length parameters for harmonic bond stretch
blen5 bond length parameters for 5-ring bond stretch
blen4 bond length parameters for 4-ring bond stretch
blen3 bond length parameters for 3-ring bond stretch
dlen electronegativity bond length correction parameters
kb string of atom classes for harmonic bond stretch
kb5 string of atom classes for 5-ring bond stretch
kb4 string of atom classes for 4-ring bond stretch
kb3 string of atom classes for 3-ring bond stretch
kel string of atom classes for electronegativity corrections
KCHRGE Module partial charge forcefield parameters
chg partial charge parameters for each atom type
KCPEN Module charge penetration forcefield parameters
cpele valence electron magnitude for each atom class
cpalp alpha charge penetration parameter for each atom class
KCTRN Module charge transfer forcefield parameters
ctchg charge transfer magnitude for each atom class
ctdmp alpha charge transfer parameter for each atom class
KDIPOL Module bond dipole forcefield parameters
maxnd maximum number of bond dipole parameter entries
maxnd5 maximum number of 5-membered ring dipole entries
maxnd4 maximum number of 4-membered ring dipole entries
maxnd3 maximum number of 3-membered ring dipole entries
dpl dipole moment parameters for bond dipoles
dpl5 dipole moment parameters for 5-ring dipoles
dpl4 dipole moment parameters for 4-ring dipoles
dpl3 dipole moment parameters for 3-ring dipoles
pos dipole position parameters for bond dipoles
pos5 dipole position parameters for 5-ring dipoles
pos4 dipole position parameters for 4-ring dipoles
pos3 dipole position parameters for 3-ring dipoles
kd string of atom classes for bond dipoles
kd5 string of atom classes for 5-ring dipoles
kd4 string of atom classes for 4-ring dipoles
kd3 string of atom classes for 3-ring dipoles
KDSP Module damped dispersion forcefield parameters
dspsix C6 dispersion coefficient for each atom class
dspdmp alpha dispersion parameter for each atom class
KEXPL Module exch-polarization forcefield parameters
pepk exchange-polarization spring constant for atom classes
peppre exchange-polarization prefactor for atom classes
pepdmp exchange-polarization damping alpha for atom classes
pepl exchange-polarization logical flag for atom classes
KEYS Module contents of the keyword control file
maxkey maximum number of lines in the keyword file
nkey number of nonblank lines in the keyword file
keyline contents of each individual keyword file line
KHBOND Module H-bonding term forcefield parameters
maxnhb maximum number of hydrogen bonding pair entries
radhb radius parameter for hydrogen bonding pairs
epshb well depth parameter for hydrogen bonding pairs
khb string of atom types for hydrogen bonding pairs
KIPROP Module improper dihedral forcefield parameters
maxndi maximum number of improper dihedral parameter entries
dcon force constant parameters for improper dihedrals
tdi ideal dihedral angle values for improper dihedrals
kdi string of atom classes for improper dihedral angles
KITORS Module improper torsion forcefield parameters
maxnti maximum number of improper torsion parameter entries
ti1 torsional parameters for improper 1-fold rotation
ti2 torsional parameters for improper 2-fold rotation
ti3 torsional parameters for improper 3-fold rotation
kti string of atom classes for improper torsional parameters
KMULTI Module atomic multipole forcefield parameters
maxnmp maximum number of atomic multipole parameter entries
multip atomic monopole, dipole and quadrupole values
mpaxis type of local axis definition for atomic multipoles
kmp string of atom types for atomic multipoles
KOPBND Module out-of-plane bend forcefield parameters
maxnopb maximum number of out-of-plane bending entries
opbn force constant parameters for out-of-plane bending
kopb string of atom classes for out-of-plane bending
KOPDST Module out-of-plane distance forcefield params
maxnopd maximum number of out-of-plane distance entries
opds force constant parameters for out-of-plane distance
kopd string of atom classes for out-of-plane distance
KORBS Module pisystem orbital forcefield parameters
maxnpi maximum number of pisystem bond parameter entries
maxnpi5 maximum number of 5-membered ring pibond entries
maxnpi4 maximum number of 4-membered ring pibond entries
sslope slope for bond stretch vs. pi-bond order
sslope5 slope for 5-ring bond stretch vs. pi-bond order
sslope4 slope for 4-ring bond stretch vs. pi-bond order
tslope slope for 2-fold torsion vs. pi-bond order
tslope5 slope for 5-ring 2-fold torsion vs. pi-bond order
tslope4 slope for 4-ring 2-fold torsion vs. pi-bond order
electron number of pi-electrons for each atom class
ionize ionization potential for each atom class
repulse repulsion integral value for each atom class
kpi string of atom classes for pisystem bonds
kpi5 string of atom classes for 5-ring pisystem bonds
kpi4 string of atom classes for 4-ring pisystem bonds
KPITOR Module pi-system torsion forcefield parameters
maxnpt maximum number of pi-system torsion parameter entries
ptcon force constant parameters for pi-system torsions
kpt string of atom classes for pi-system torsion terms
KPOLPR Module special Thole forcefield parameters
maxnpp maximum number of special pair polarization entries
thlpr Thole damping values for special polarization pairs
thdpr Thole direct damping for special polarization pairs
kppr string of atom types for special polarization pairs
KPOLR Module polarizability forcefield parameters
pgrp connected types in polarization group of each atom type
polr dipole polarizability parameters for each atom type
athl Thole polarizability damping value for each atom type
dthl alternate Thole direct polarization damping values
KREPL Module Pauli repulsion forcefield parameters
prsiz Pauli repulsion size value for each atom class
prdmp alpha Pauli repulsion parameter for each atom class
prele number of valence electrons for each atom class
KSTBND Module stretch-bend forcefield parameters
maxnsb maximum number of stretch-bend parameter entries
stbn force constant parameters for stretch-bend terms
ksb string of atom classes for stretch-bend terms
KSTTOR Module stretch-torsion forcefield parameters
maxnbt maximum number of stretch-torsion parameter entries
btcon torsional amplitude parameters for stretch-torsion
kbt string of atom classes for stretch-torsion terms
KTORSN Module torsional angle forcefield parameters
maxnt maximum number of torsional angle parameter entries
maxnt5 maximum number of 5-membered ring torsion entries
maxnt4 maximum number of 4-membered ring torsion entries
t1 torsional parameters for standard 1-fold rotation
t2 torsional parameters for standard 2-fold rotation
t3 torsional parameters for standard 3-fold rotation
t4 torsional parameters for standard 4-fold rotation
t5 torsional parameters for standard 5-fold rotation
t6 torsional parameters for standard 6-fold rotation
t15 torsional parameters for 1-fold rotation in 5-ring
t25 torsional parameters for 2-fold rotation in 5-ring
t35 torsional parameters for 3-fold rotation in 5-ring
t45 torsional parameters for 4-fold rotation in 5-ring
t55 torsional parameters for 5-fold rotation in 5-ring
t65 torsional parameters for 6-fold rotation in 5-ring
t14 torsional parameters for 1-fold rotation in 4-ring
t24 torsional parameters for 2-fold rotation in 4-ring
t34 torsional parameters for 3-fold rotation in 4-ring
t44 torsional parameters for 4-fold rotation in 4-ring
t54 torsional parameters for 5-fold rotation in 4-ring
t64 torsional parameters for 6-fold rotation in 4-ring
kt string of atom classes for torsional angles
kt5 string of atom classes for 5-ring torsions
kt4 string of atom classes for 4-ring torsions
KTRTOR Module torsion-torsion forcefield parameters
maxntt maximum number of torsion-torsion parameter entries
maxtgrd maximum dimension of torsion-torsion spline grid
maxtgrd2 maximum number of torsion-torsion spline grid points
tnx number of columns in torsion-torsion spline grid
tny number of rows in torsion-torsion spline grid
ttx angle values for first torsion of spline grid
tty angle values for second torsion of spline grid
tbf function values at points on spline grid
tbx gradient over first torsion of spline grid
tby gradient over second torsion of spline grid
tbxy Hessian cross components over spline grid
ktt string of torsion-torsion atom classes
KURYBR Module Urey-Bradley term forcefield parameters
maxnu maximum number of Urey-Bradley parameter entries
ucon force constant parameters for Urey-Bradley terms
dst13 ideal 1-3 distance parameters for Urey-Bradley terms
ku string of atom classes for Urey-Bradley terms
KVDWPR Module special pair vdw forcefield parameters
maxnvp maximum number of special van der Waals pair entries
radpr radius parameter for special van der Waals pairs
epspr well depth parameter for special van der Waals pairs
kvpr string of atom classes for special van der Waals pairs
KVDWS Module van der Waals term forcefield parameters
rad van der Waals radius parameter for each atom 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
intmax maximum number of interpolations during line search
stpmin minimum step length in current line search direction
stpmax maximum step length in current line search direction
cappa stringency of line search (0=tight < cappa < 1=loose)
slpmax projected gradient above which stepsize is reduced
angmax maximum angle between search direction and -gradient
MATH Module mathematical and geometrical constants
pi numerical value of the geometric constant
elog numerical value of the natural logarithm base
radian conversion factor from radians to degrees
logten numerical value of the natural log of ten
twosix numerical value of the sixth root of two
sqrtpi numerical value of the square root of Pi
sqrttwo numerical value of the square root of two
sqrtthree numerical value of the square root of three
MDSTUF Module molecular dynamics trajectory controls
nfree total number of degrees of freedom for a system
irest steps between removal of COM motion (0=no removal)
bmnmix mixing coefficient for use with Beeman integrator
nrespa inner steps per outer step for RESPA integrator
arespa inner time step for use with RESPA integrator
dorest logical flag to remove center of mass motion
integrate type of molecular dynamics integration algorithm
MERCK Module MMFF-specific force field parameters
nlignes number of atom pairs having MMFF Bond Type 1
bt_1 atom pairs having MMFF Bond Type 1
eqclass table of atom class equivalencies used to find
default parameters if explicit values are missing
see J. Comput. Chem., 17, 490-519, '95, Table IV)
crd number of attached neighbors |
val valency value | see T. A. Halgren,
pilp if 0, no lone pair | J. Comput. Chem.,
if 1, one or more lone pair(s) | 17, 616-645 (1995)
mltb multibond indicator |
arom aromaticity indicator |
lin linearity indicator |
sbmb single- vs multiple-bond flag |
mmffarom aromatic rings parameters
mmffaromc cationic aromatic rings parameters
mmffaroma anionic aromatic rings parameters
MINIMA Module general parameters for minimizations
nextiter iteration number to use for the first iteration
fctmin value below which function is deemed optimized
hguess initial value for the H-matrix diagonal elements
maxiter maximum number of iterations during optimization
MOLCUL Module individual molecules in current system
nmol total number of separate molecules in the system
imol first and last atom of each molecule in the list
kmol contiguous list of the atoms in each molecule
molcule number of the molecule to which each atom belongs
totmass total weight of all the molecules in the system
molmass molecular weight for each molecule in the system
MOLDYN Module MD trajectory velocity & acceleration
v current velocity of each atom along the x,y,z-axes
a current acceleration of each atom along x,y,z-axes
aalt alternate acceleration of each atom along x,y,z-axes
MOMENT Module electric multipole moment components
netchg net electric charge for the total system
netdpl dipole moment magnitude for the total system
netqdp diagonal quadrupole (Qxx, Qyy, Qzz) for system
xdpl dipole vector x-component in the global frame
ydpl dipole vector y-component in the global frame
zdpl dipole vector z-component in the global frame
xxqdp quadrupole tensor xx-component in global frame
xyqdp quadrupole tensor xy-component in global frame
xzqdp quadrupole tensor xz-component in global frame
yxqdp quadrupole tensor yx-component in global frame
yyqdp quadrupole tensor yy-component in global frame
yzqdp quadrupole tensor yz-component in global frame
zxqdp quadrupole tensor zx-component in global frame
zyqdp quadrupole tensor zy-component in global frame
zzqdp quadrupole tensor zz-component in global frame
MPLPOT Module multipole functional form details
m2scale scale factor for 1-2 multipole energy interactions
m3scale scale factor for 1-3 multipole energy interactions
m4scale scale factor for 1-4 multipole energy interactions
m5scale scale factor for 1-5 multipole energy interactions
use_chgpen flag to use charge penetration damped potential
pentyp type of penetration damping (NONE, GORDON1, GORDON2)
MPOLE Module atomic multipoles in current structure
maxpole max components (monopole=1,dipole=4,quadrupole=13)
npole total number of multipole sites in the system
ipole number of the atom for each multipole site
polsiz number of multipole components at each atom
pollist multipole site for each atom (0=no multipole)
zaxis number of the z-axis defining atom for each atom
xaxis number of the x-axis defining atom for each atom
yaxis number of the y-axis defining atom for each atom
pole local frame Cartesian multipoles for each atom
rpole global frame Cartesian multipoles for each atom
mono0 original atomic monopole values for charge flux
polaxe local coordinate frame type for each atom
MRECIP Module reciprocal PME for permanent multipoles
vmxx scalar sum xx-component of virial due to multipoles
vmyy scalar sum yy-component of virial due to multipoles
vmzz scalar sum zz-component of virial due to multipoles
vmxy scalar sum xy-component of virial due to multipoles
vmxz scalar sum xz-component of virial due to multipoles
vmyz scalar sum yz-component of virial due to multipoles
cmp Cartesian permenent multipoles as polytensor vector
fmp fractional permanent multipoles as polytensor vector
cphi Cartesian permanent multipole potential and field
fphi fractional permanent multipole potential and field
MUTANT Module free energy calculation hybrid atoms
nmut number of atoms mutated from initial to final state
vcouple van der Waals lambda type (0=decouple, 1=annihilate)
imut atomic sites differing in initial and final state
type0 atom type of each atom in the initial state system
class0 atom class of each atom in the initial state system
type1 atom type of each atom in the final state system
class1 atom class of each atom in the final state system
lambda generic weighting between initial and final states
vlambda state weighting value for van der Waals potentials
elambda state weighting value for electrostatic potentials
tlambda state weighting value for torsional potential
scexp scale factor for soft core buffered 14-7 potential
scalpha scale factor for soft core buffered 14-7 potential
mut true if an atom is to be mutated, false otherwise
NEIGH Module pairwise neighbor list indices & storage
maxvlst maximum size of van der Waals pair neighbor lists
maxelst maximum size of electrostatic pair neighbor lists
maxulst maximum size of dipole preconditioner pair lists
nvlst number of sites in list for each vdw site
vlst site numbers in neighbor list of each vdw site
nelst number of sites in list for each electrostatic site
elst site numbers in list of each electrostatic site
nulst number of sites in list for each preconditioner site
ulst site numbers in list of each preconditioner site
lbuffer width of the neighbor list buffer region
pbuffer width of the preconditioner list buffer region
lbuf2 square of half the neighbor list buffer width
pbuf2 square of half the preconditioner list buffer width
vbuf2 square of van der Waals cutoff plus the list buffer
vbufx square of van der Waals cutoff plus 2X list buffer
dbuf2 square of dispersion cutoff plus the list buffer
dbufx square of dispersion cutoff plus 2X list buffer
cbuf2 square of charge cutoff plus the list buffer
cbufx square of charge cutoff plus 2X list buffer
mbuf2 square of multipole cutoff plus the list buffer
mbufx square of multipole cutoff plus 2X list buffer
ubuf2 square of preconditioner cutoff plus the list buffer
ubufx square of preconditioner cutoff plus 2X list buffer
xvold x-coordinate at last vdw/dispersion list update
yvold y-coordinate at last vdw/dispersion list update
zvold z-coordinate at last vdw/dispersion list update
xeold x-coordinate at last electrostatic list update
yeold y-coordinate at last electrostatic list update
zeold z-coordinate at last electrostatic list update
xuold x-coordinate at last preconditioner list update
yuold y-coordinate at last preconditioner list update
zuold z-coordinate at last preconditioner list update
dovlst logical flag to rebuild vdw neighbor list
dodlst logical flag to rebuild dispersion neighbor list
doclst logical flag to rebuild charge neighbor list
domlst logical flag to rebuild multipole neighbor list
doulst logical flag to rebuild preconditioner neighbor list
NONPOL Module nonpolar cavity & dispersion parameters
epso water oxygen eps for implicit dispersion term
epsh water hydrogen eps for implicit dispersion term
rmino water oxygen Rmin for implicit dispersion term
rminh water hydrogen Rmin for implicit dispersion term
awater water number density at standard temp & pressure
slevy enthalpy-to-free energy scale factor for dispersion
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 for coordinates in Tinker XYZ format
binary logical flag for coordinates in DCD binary format
noversion logical flag governing use of filename versions
overwrite logical flag to overwrite intermediate files inplace
arcsave logical flag to save coordinates in Tinker XYZ format
dcdsave logical flag to save coordinates in DCD binary format
cyclesave logical flag to mark use of numbered cycle files
velsave logical flag to save velocity vector components
frcsave logical flag to save force vector components
uindsave logical flag to save induced atomic dipoles
coordtype selects Cartesian, internal, rigid body or none
PARAMS Module force field parameter file contents
maxprm maximum number of lines in the parameter file
nprm number of nonblank lines in the parameter file
prmline contents of each individual parameter file line
PATHS Module Elber reaction path method parameters
pnorm length of the reactant-product vector
acoeff transformation matrix 'A' from Elber algorithm
pc0 reactant Cartesian coordinates as variables
pc1 product Cartesian coordinates as variables
pvect vector connecting the reactant and product
pstep step per cycle along reactant-product vector
pzet current projection on reactant-product vector
gc gradient of the path constraints
PBSTUF Module Poisson-Boltzmann solvation parameters
APBS configuration parameters (see APBS documentation for details). In the column on the right are possible values for each variable, with default values given in brackets. Only a subset of the APBS options are supported and/or are appropriate for use with AMOEBA.
pbtyp lpbe
pbsoln mg-auto, [mg-manual]
bcfl boundary conditions zero, sdh, [mdh]
chgm multipole discretization spl4
srfm surface method mol, smol, [spl4]
dime number of grid points [65, 65, 65]
grid grid spacing (mg-manual) fxn of "dime"
cgrid coarse grid spacing fxn of "dime"
fgrid fine grid spacing cgrid / 2
gcent grid center (mg-manual) center of mass
cgcent coarse grid center center of mass
fgcent fine grid center center of mass
pdie solute/homogeneous dieletric [1.0]
sdie solvent dieletric [78.3]
ionn number of ion species [0]
ionc ion concentration (M) [0.0]
ionq ion charge (electrons) [1.0]
ionr ion radius (A) [2.0]
srad solvent probe radius (A) [1.4]
swin surface spline window width [0.3]
sdens density of surface points [10.0]
smin minimum distance between an [10.0]
pbe Poisson-Boltzmann permanent multipole solvation energy
apbe Poisson-Boltzmann permanent multipole energy over atoms
pbr Poisson-Boltzmann cavity radii for atom types
pbep Poisson-Boltzmann energies on permanent multipoles
pbfp Poisson-Boltzmann forces on permanent multipoles
pbtp Poisson-Boltzmann torques on permanent multipoles
pbeuind Poisson-Boltzmann field due to induced dipoles
pbeuinp Poisson-Boltzmann field due to non-local induced dipoles
PDB Module Protein Data Bank structure definition
npdb number of atoms stored in Protein Data Bank format
nres number of residues stored in Protein Data Bank format
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 atom for each polarizable site
jpolar index into polarization parameter matrix for each atom
polarity dipole polarizability for each atom site (Ang**3)
thole Thole polarization damping value for each atom
tholed Thole direct polarization damping value for each atom
pdamp value of polarizability scale factor for each atom
thlval Thole damping parameter value for each atom type pair
thdval alternate Thole direct damping value for atom type pair
udir direct induced dipole components for each atom site
udirp direct induced dipoles in field used for energy terms
udirs direct GK or PB induced dipoles for each atom site
udirps direct induced dipoles in field used for GK or PB energy
uind mutual induced dipole components for each atom site
uinp mutual induced dipoles in field used for energy terms
uinds mutual GK or PB induced dipoles for each atom site
uinps mutual induced dipoles in field used for GK or PB energy
uexact exact SCF induced dipoles to full numerical precision
douind flag to allow induced dipoles at each atom site
POLGRP Module polarization group connectivity lists
maxp11 maximum number of atoms in a polarization group
maxp12 maximum number of atoms in groups 1-2 to an atom
maxp13 maximum number of atoms in groups 1-3 to an atom
maxp14 maximum number of atoms in groups 1-4 to an atom
np11 number of atoms in polarization group of each atom
np12 number of atoms in groups 1-2 to each atom
np13 number of atoms in groups 1-3 to each atom
np14 number of atoms in groups 1-4 to each atom
ip11 atom numbers of atoms in same group as each atom
ip12 atom numbers of atoms in groups 1-2 to each atom
ip13 atom numbers of atoms in groups 1-3 to each atom
ip14 atom numbers of atoms in groups 1-4 to each atom
POLOPT Module induced dipoles for OPT extrapolation
maxopt maximum order for OPT induced dipole extrapolation
optorder highest coefficient order for OPT dipole extrapolation
optlevel current OPT order for reciprocal potential and field
copt coefficients for OPT total induced dipole moments
copm coefficients for OPT incremental induced dipole moments
uopt OPT induced dipole components at each multipole site
uoptp OPT induced dipoles in field used for energy terms
uopts OPT GK or PB induced dipoles at each multipole site
uoptps OPT induced dipoles in field used for GK or PB energy
fopt OPT fractional reciprocal potentials at multipole sites
foptp OPT fractional reciprocal potentials for energy terms
POLPCG Module induced dipoles via the PCG solver
mindex index into preconditioner inverse for PCG solver
pcgpeek value of acceleration factor for PCG peek step
minv preconditioner inverse for induced dipole PCG solver
pcgprec flag to allow use of preconditioner with PCG solver
pcgguess flag to use initial PCG based on direct field
POLPOT Module polarization functional form details
politer maximum number of induced dipole SCF iterations
poleps induced dipole convergence criterion (rms Debye/atom)
p2scale scale factor for 1-2 polarization energy interactions
p3scale scale factor for 1-3 polarization energy interactions
p4scale scale factor for 1-4 polarization energy interactions
p5scale scale factor for 1-5 polarization energy interactions
p2iscale scale factor for 1-2 intragroup polarization energy
p3iscale scale factor for 1-3 intragroup polarization energy
p4iscale scale factor for 1-4 intragroup polarization energy
p5iscale scale factor for 1-5 intragroup polarization energy
d1scale scale factor for intra-group direct induction
d2scale scale factor for 1-2 group direct induction
d3scale scale factor for 1-3 group direct induction
d4scale scale factor for 1-4 group direct induction
u1scale scale factor for intra-group mutual induction
u2scale scale factor for 1-2 group mutual induction
u3scale scale factor for 1-3 group mutual induction
u4scale scale factor for 1-4 group mutual induction
w2scale scale factor for 1-2 induced dipole interactions
w3scale scale factor for 1-3 induced dipole interactions
w4scale scale factor for 1-4 induced dipole interactions
w5scale scale factor for 1-5 induced dipole interactions
udiag acceleration factor for induced dipole SCF iterations
dpequal flag to set dscale values equal to pscale values
use_thole flag to use Thole damped polarization interactions
use_tholed flag to use alternate Thole for direct polarization
use_expol flag to use damped exchange polarization correction
poltyp type of polarization (MUTUAL, DIRECT, OPT or TCG)
POLTCG Module induced dipoles via the TCG solver
tcgorder total number of TCG iterations to be used
tcgnab number of mutual induced dipole components
tcgpeek value of acceleration factor for TCG peek step
uad left-hand side mutual induced d-dipoles
uap left-hand side mutual induced p-dipoles
ubd right-hand side mutual induced d-dipoles
ubp right-hand side mutual induced p-dipoles
tcgguess flag to use initial TCG based on direct field
POTENT Module usage of potential energy components
use_bond logical flag governing use of bond stretch potential
use_angle logical flag governing use of angle bend potential
use_strbnd logical flag governing use of stretch-bend potential
use_urey logical flag governing use of Urey-Bradley potential
use_angang logical flag governing use of angle-angle cross term
use_opbend logical flag governing use of out-of-plane bend term
use_opdist logical flag governing use of out-of-plane distance
use_improp logical flag governing use of improper dihedral term
use_imptor logical flag governing use of improper torsion term
use_tors logical flag governing use of torsional potential
use_pitors logical flag governing use of pi-system torsion term
use_strtor logical flag governing use of stretch-torsion term
use_angtor logical flag governing use of angle-torsion term
use_tortor logical flag governing use of torsion-torsion term
use_vdw logical flag governing use of van der Waals potential
use_repel logical flag governing use of Pauli repulsion term
use_disp logical flag governing use of dispersion potential
use_charge logical flag governing use of charge-charge potential
use_chgdpl logical flag governing use of charge-dipole potential
use_dipole logical flag governing use of dipole-dipole potential
use_mpole logical flag governing use of multipole potential
use_polar logical flag governing use of polarization term
use_chgtrn logical flag governing use of charge transfer term
use_chgflx logical flag governing use of charge flux term
use_rxnfld logical flag governing use of reaction field term
use_solv logical flag governing use of continuum solvation term
use_metal logical flag governing use of ligand field term
use_geom logical flag governing use of geometric restraints
use_extra logical flag governing use of extra potential term
use_born logical flag governing use of Born radii values
use_orbit logical flag governing use of pisystem computation
use_mutate logical flag governing use of hybrid potential terms
POTFIT Module values for electrostatic potential fit
nconf total number of configurations to be analyzed
namax maximum number of atoms in the largest configuration
ngatm total number of atoms with active potential grid points
nfatm total number of atoms in electrostatic potential fit
npgrid total number of electrostatic potential grid points
ipgrid atom associated with each potential grid point
resp weight used to restrain parameters to original values
xdpl0 target x-component of molecular dipole moment
ydpl0 target y-component of molecular dipole moment
zdpl0 target z-component of molecular dipole moment
xxqdp0 target xx-component of molecular quadrupole moment
xyqdp0 target xy-component of molecular quadrupole moment
xzqdp0 target xz-component of molecular quadrupole moment
yyqdp0 target yy-component of molecular quadrupole moment
yzqdp0 target yz-component of molecular quadrupole moment
zzqdp0 target zz-component of molecular quadrupole moment
fit0 initial value of each parameter used in potential fit
fchg partial charges by atom type during potential fit
fpol atomic multipoles by atom type during potential fit
pgrid Cartesian coordinates of potential grid points
epot values of electrostatic potential at grid points
use_dpl flag to include molecular dipole in potential fit
use_qdp flag to include molecular quadrupole in potential fit
fit_mpl flag for atomic monopoles to vary in potential fit
fit_dpl flag for atomic dipoles to vary in potential fit
fit_qdp flag for atomic quadrupoles to vary in potential fit
fit_chgpen flag for charge penetration to vary in potential fit
fitchg flag marking atom types used in partial charge fit
fitpol flag marking atom types used in atomic multipole fit
fitcpen flag marking atom types used in charge penetration
gatm flag to use potential grid points around each atom
fatm flag to use each atom in electrostatic potential fit
resptyp electrostatic restraint target (ORIG, ZERO or NONE)
varpot descriptive name for each variable in potential fit
PTABLE Module symbols and info for chemical elements
maxele maximum number of elements from periodic table
atmass standard atomic weight for each chemical element
vdwrad van der Waals radius for each chemical element
covrad covalent radius for each chemical element
elemnt atomic symbol for each chemical element
REFER Module reference atomic coordinate storage
nref total number of atoms in each reference system
refltitle length in characters of reference title lines
refleng length in characters of reference base filenames
reftyp atom types of the atoms in each reference system
n12ref number of atoms bonded to each reference atom
i12ref atom numbers of atoms 1-2 connected to each atom
xboxref reference a-axis length of periodic box
yboxref reference b-axis length of periodic box
zboxref reference c-axis length of periodic box
alpharef reference angle between b- and c-axes of box
betaref reference angle between a- and c-axes of box
gammaref reference angle between a- and b-axes of box
xref reference x-coordinates for atoms in each system
yref reference y-coordinates for atoms in each system
zref reference z-coordinates for atoms in each system
refnam atom names of the atoms in each reference system
reffile full filename for each reference system
reftitle title used to describe each reference system
REPEL Module Pauli repulsion for current structure
nrep total number of repulsion sites in the system
irep number of the atom for each repulsion site
replist repulsion multipole site for each atom (0=none)
sizpr Pauli repulsion size parameter value for each atom
dmppr Pauli repulsion alpha damping value for each atom
elepr Pauli repulsion valence electrons for each atom
repole repulsion Cartesian multipoles in the local frame
rrepole repulsion Cartesian multipoles in the global frame
REPPOT Module repulsion interaction scale factors
r2scale scale factor for 1-2 repulsion energy interactions
r3scale scale factor for 1-3 repulsion energy interactions
r4scale scale factor for 1-4 repulsion energy interactions
r5scale scale factor for 1-5 repulsion energy interactions
RESDUE Module amino acid & nucleotide residue names
maxamino maximum number of amino acid residue types
maxnuc maximum number of nucleic acid residue types
ntyp biotypes for mid-chain peptide backbone N atoms
catyp biotypes for mid-chain peptide backbone CA atoms
ctyp biotypes for mid-chain peptide backbone C atoms
hntyp biotypes for mid-chain peptide backbone HN atoms
otyp biotypes for mid-chain peptide backbone O atoms
hatyp biotypes for mid-chain peptide backbone HA atoms
cbtyp biotypes for mid-chain peptide backbone CB atoms
nntyp biotypes for N-terminal peptide backbone N atoms
cantyp biotypes for N-terminal peptide backbone CA atoms
cntyp biotypes for N-terminal peptide backbone C atoms
hnntyp biotypes for N-terminal peptide backbone HN atoms
ontyp biotypes for N-terminal peptide backbone O atoms
hantyp biotypes for N-terminal peptide backbone HA atoms
nctyp biotypes for C-terminal peptide backbone N atoms
cactyp biotypes for C-terminal peptide backbone CA atoms
cctyp biotypes for C-terminal peptide backbone C atoms
hnctyp biotypes for C-terminal peptide backbone HN atoms
octyp biotypes for C-terminal peptide backbone O atoms
hactyp biotypes for C-terminal peptide backbone HA atoms
o5typ biotypes for nucleotide backbone and sugar O5' atoms
c5typ biotypes for nucleotide backbone and sugar C5' atoms
h51typ biotypes for nucleotide backbone and sugar H5' atoms
h52typ biotypes for nucleotide backbone and sugar H5'' atoms
c4typ biotypes for nucleotide backbone and sugar C4' atoms
h4typ biotypes for nucleotide backbone and sugar H4' atoms
o4typ biotypes for nucleotide backbone and sugar O4' atoms
c1typ biotypes for nucleotide backbone and sugar C1' atoms
h1typ biotypes for nucleotide backbone and sugar H1' atoms
c3typ biotypes for nucleotide backbone and sugar C3' atoms
h3typ biotypes for nucleotide backbone and sugar H3' atoms
c2typ biotypes for nucleotide backbone and sugar C2' atoms
h21typ biotypes for nucleotide backbone and sugar H2' atoms
o2typ biotypes for nucleotide backbone and sugar O2' atoms
h22typ biotypes for nucleotide backbone and sugar H2'' atoms
o3typ biotypes for nucleotide backbone and sugar O3' atoms
ptyp biotypes for nucleotide backbone and sugar P atoms
optyp biotypes for nucleotide backbone and sugar OP atoms
h5ttyp biotypes for nucleotide backbone and sugar H5T atoms
h3ttyp biotypes for nucleotide backbone and sugar H3T atoms
amino three-letter abbreviations for amino acids types
nuclz three-letter abbreviations for nucleic acids types
amino1 one-letter abbreviations for amino acids types
nuclz1 one-letter abbreviations for nucleic acids types
RESTRN Module parameters for geometrical restraints
npfix number of position restraints to be applied
ndfix number of distance restraints to be applied
nafix number of angle restraints to be applied
ntfix number of torsional restraints to be applied
ngfix number of group distance restraints to be applied
nchir number of chirality restraints to be applied
ipfix atom number involved in each position restraint
kpfix flags to use x-, y-, z-coordinate position restraints
idfix atom numbers defining each distance restraint
iafix atom numbers defining each angle restraint
itfix atom numbers defining each torsional restraint
igfix group numbers defining each group distance restraint
ichir atom numbers defining each chirality restraint
depth depth of shallow Gaussian basin restraint
width exponential width coefficient of Gaussian basin
rwall radius of spherical droplet boundary restraint
xpfix x-coordinate target for each restrained position
ypfix y-coordinate target for each restrained position
zpfix z-coordinate target for each restrained position
pfix force constant and flat-well range for each position
dfix force constant and target range for each distance
afix force constant and target range for each angle
tfix force constant and target range for each torsion
gfix force constant and target range for each group distance
chir force constant and target range for chiral centers
use_basin logical flag governing use of Gaussian basin
use_wall logical flag governing use of droplet boundary
RGDDYN Module rigid body MD velocities and momenta
xcmo x-component from each atom to center of rigid body
ycmo y-component from each atom to center of rigid body
zcmo z-component from each atom to center of rigid body
vcm current translational velocity of each rigid body
wcm current angular velocity of each rigid body
lm current angular momentum of each rigid body
vc half-step translational velocity for kinetic energy
wc half-step angular velocity for kinetic energy
linear logical flag to mark group as linear or nonlinear
RIGID Module rigid body coordinates for atom groups
xrb rigid body reference x-coordinate for each atom
yrb rigid body reference y-coordinate for each atom
zrb rigid body reference z-coordinate for each atom
rbc current rigid body coordinates for each group
use_rigid flag to mark use of rigid body coordinate system
RING Module number and location of ring structures
nring3 total number of 3-membered rings in the system
nring4 total number of 4-membered rings in the system
nring5 total number of 5-membered rings in the system
nring6 total number of 6-membered rings in the system
nring7 total number of 7-membered rings in the system
iring3 numbers of the atoms involved in each 3-ring
iring4 numbers of the atoms involved in each 4-ring
iring5 numbers of the atoms involved in each 5-ring
iring6 numbers of the atoms involved in each 6-ring
iring7 numbers of the atoms involved in each 7-ring
ROTBND Module molecule partitions for bond rotation
nrot total number of atoms moving when bond rotates
rot atom numbers of atoms moving when bond rotates
use_short logical flag governing use of shortest atom list
RXNFLD Module reaction field matrix and indices
ijk indices into the reaction field element arrays
b1 first reaction field matrix element array
b2 second reaction field matrix element array
RXNPOT Module reaction field functional form details
rfsize radius of reaction field sphere centered at origin
rfbulkd bulk dielectric constant of reaction field continuum
rfterms number of terms to use in reaction field summation
SCALES Module optimization parameter scale factors
scale multiplicative factor for each optimization parameter
set_scale logical flag to show if scale factors have been set
SEQUEN Module sequence information for biopolymer
nseq total number of residues in biopolymer sequences
nchain number of separate biopolymer sequence chains
ichain first and last residue in each biopolymer chain
seqtyp residue type for each residue in the sequence
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
maxatm maximum number of atoms in the molecular system
maxtyp maximum number of force field atom type definitions
maxclass maximum number of force field atom class definitions
maxval maximum number of atoms directly bonded to an atom
maxref maximum number of stored reference molecular systems
maxgrp maximum number of user-defined groups of atoms
maxres maximum number of residues in the macromolecule
maxfix maximum number of geometric constraints and restraints
maxbio maximum number of biopolymer atom definitions
SOCKET Module socket communication control parameters
skttyp socket information type (1=DYN, 2=OPT)
cstep current dynamics or optimization step number
cdt current dynamics cumulative simulation time
cenergy current potential energy from simulation
sktstart logical flag to indicate socket initialization
sktstop logical flag to indicate socket shutdown
use_socket logical flag governing use of external sockets
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
avogadro Avogadro's number (N) in particles/mole
lightspd speed of light in vacuum (c) in cm/ps
boltzmann Boltzmann constant (kB) in g*Ang**2/ps**2/mole/K
gasconst ideal gas constant (R) in kcal/mole/K
elemchg elementary charge of a proton in Coulombs
vacperm vacuum permittivity (electric constant, eps0) in F/m
emass mass of an electron in atomic mass units
planck Planck's constant (h) in J-s
joule conversion from calorie to joule
ekcal conversion from kcal to g*Ang**2/ps**2
bohr conversion from Bohr to Angstrom
hartree conversion from Hartree to kcal/mole
evolt conversion from Hartree to electron-volt
efreq conversion from Hartree to cm-1
coulomb conversion from electron**2/Ang to kcal/mole
elefield conversion from electron**2/Ang to megavolt/cm
debye conversion from electron-Ang to Debye
prescon conversion from kcal/mole/Ang**3 to Atm
UPRIOR Module previous values of induced dipoles
maxpred maximum number of predictor induced dipoles to save
nualt number of sets of prior induced dipoles in storage
maxualt number of sets of induced dipoles needed for predictor
gear coefficients for Gear predictor binomial method
aspc coefficients for always stable predictor-corrector
bpred coefficients for induced dipole predictor polynomial
bpredp coefficients for predictor polynomial in energy field
bpreds coefficients for predictor for PB/GK solvation
bpredps coefficients for predictor in PB/GK energy field
udalt prior values for induced dipoles at each site
upalt prior values for induced dipoles in energy field
usalt prior values for induced dipoles for PB/GK solvation
upsalt prior values for induced dipoles in PB/GK energy field
use_pred flag to control use of induced dipole prediction
polpred type of predictor polynomial (GEAR, ASPC or LSQR)
UREY Module Urey-Bradley interactions in structure
nurey total number of Urey-Bradley terms in the system
iury numbers of the atoms in each Urey-Bradley interaction
uk Urey-Bradley force constants (kcal/mole/Ang**2)
ul ideal 1-3 distance values in Angstroms
URYPOT Module Urey-Bradley functional form details
cury cubic coefficient in Urey-Bradley potential
qury quartic coefficient in Urey-Bradley potential
ureyunit convert Urey-Bradley energy to kcal/mole
USAGE Module atoms active during energy computation
nuse total number of active atoms in energy calculation
iuse numbers of the atoms active in energy calculation
use true if an atom is active, false if inactive
VALFIT Module valence term parameter fitting values
fit_bond logical flag to fit bond stretch parameters
fit_angle logical flag to fit angle bend parameters
fit_strbnd logical flag to fit stretch-bend parameters
fit_urey logical flag to fit Urey-Bradley parameters
fit_opbend logical flag to fit out-of-plane bend parameters
fit_tors logical flag to fit torsional parameters
fit_struct logical flag to structure-fit valence parameters
fit_force logical flag to force-fit valence parameters
VDW Module van der Waals terms in current structure
nvdw total number van der Waals sites in the system
ivdw number of the atom for each van der Waals site
jvdw index into the vdw parameter matrix for each atom
mvdw index into the vdw parameter matrix for each class
ired attached atom from which reduction factor is applied
kred value of reduction factor parameter for each atom
xred reduced x-coordinate for each atom in the system
yred reduced y-coordinate for each atom in the system
zred reduced z-coordinate for each atom in the system
radmin minimum energy distance for each atom class pair
epsilon well depth parameter for each atom class pair
radmin4 minimum energy distance for 1-4 interaction pairs
epsilon4 well depth parameter for 1-4 interaction pairs
radhbnd minimum energy distance for hydrogen bonding pairs
epshbnd well depth parameter for hydrogen bonding pairs
VDWPOT Module van der Waals functional form details
igauss coefficients of Gaussian fit to vdw potential
ngauss number of Gaussians used in fit to vdw potential
abuck value of "A" constant in Buckingham vdw potential
bbuck value of "B" constant in Buckingham vdw potential
cbuck value of "C" constant in Buckingham vdw potential
ghal value of "gamma" in buffered 14-7 vdw potential
dhal value of "delta" in buffered 14-7 vdw potential
v2scale factor by which 1-2 vdw interactions are scaled
v3scale factor by which 1-3 vdw interactions are scaled
v4scale factor by which 1-4 vdw interactions are scaled
v5scale factor by which 1-5 vdw interactions are scaled
use_vcorr flag to use long range van der Waals correction
vdwindex indexing mode (atom type or class) for vdw parameters
vdwtyp type of van der Waals potential energy function
radtyp type of parameter (sigma or R-min) for atomic size
radsiz atomic size provided as radius or diameter
radrule combining rule for atomic size parameters
epsrule combining rule for vdw well depth parameters
gausstyp type of Gaussian fit to van der Waals potential
VIBS Module iterative vibrational analysis components
rho trial vectors for iterative vibrational analysis
rhok alternate vectors for iterative vibrational analysis
rwork temporary work array for eigenvector transformation
VIRIAL Module components of internal virial tensor
vir total internal virial Cartesian tensor components
use_virial logical flag governing use of virial computation
WARP Module potential surface smoothing parameters
deform value of the smoothing deformation parameter
difft diffusion coefficient for torsional potential
diffv diffusion coefficient for van der Waals potential
diffc diffusion coefficient for charge-charge potential
m2 second moment of the GDA gaussian for each atom
use_smooth flag to use a potential energy smoothing method
use_dem flag to use diffusion equation method potential
use_gda flag to use gaussian density annealing potential
use_tophat flag to use analytical tophat smoothed potential
use_stophat flag to use shifted tophat smoothed potential
XTALS Module structures used for parameter fitting
maxlsq maximum number of least squares variables
maxrsd maximum number of residual functions
nxtal number of molecular structures to be stored
nvary number of potential parameters to optimize
ivary index for the types of potential parameters
iresid structure to which each residual function refers
vary atom numbers involved in potential parameters
e0_lattice ideal lattice energy for the current crystal
varxtl type of each potential parameter to be optimized
rsdxtl experimental variable for each of the residuals
ZCLOSE Module Z-matrix ring openings and closures
nadd number of added bonds between Z-matrix atoms
ndel number of bonds between Z-matrix bonds to delete
iadd numbers of the atom pairs defining added bonds
idel numbers of the atom pairs defining deleted bonds
ZCOORD Module Z-matrix internal coordinate values
iz defining atom numbers for each Z-matrix atom
zbond bond length used to define each Z-matrix atom
zang bond angle used to define each Z-matrix atom
ztors angle or torsion used to define Z-matrix atom