# Description of 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 computed
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-orbital torsion energy terms computed
nebt number of stretch-torsion energy terms computed
nett number of torsion-torsion energy terms computed
nev number of van der Waals 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
new number of Ewald summation energy terms computed
ner 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 Modules - information for superposition of structures
wfit weights assigned to atom pairs during superposition
nfit number of atoms to use in superimposing two structures
ifit atom numbers of pairs of atoms to be superimposed

ANALYZ energy components partitioned over 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-orbital torsion energy partitioned over atoms aebt stretch-torsion energy partitioned over atoms aett torsion-torsion energy partitioned over atoms aev van der Waals 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 aer 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 angle-angle terms in current structure

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

ANGLE bond angles within the current structure

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

ANGPOT specifics of bond angle functional forms

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 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 mm2stbn logical flag governing use of MM2-style stretch-bend

ARGUE command line arguments at program startup

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

ATMLST local geometry terms involving each atom

bndlist list of the bond numbers involving each atom anglist list of the angle numbers centered on each atom

ATMTYP atomic properties for each current atom

mass atomic weight for each atom in the system 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 name atom name for each atom in the system story descriptive type for each atom in system

ATOMS number, position and type of current atoms

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 n total number of atoms in the current system type atom type number for each atom in the system

BATH temperature and pressure control parameters

maxnose maximum length of the Nose-Hoover chain kelvin0 target value for the system temperature (K) kelvin variable target temperature for thermostat (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 xnh position of each chained Nose-Hoover thermostat vnh velocity of each chained Nose-Hoover thermostat qnh mass for each chained Nose-Hoover thermostat gnh coupling between chained Nose-Hoover thermostats isothermal logical flag governing use of temperature control isobaric logical flag governing use of pressure control tempvary logical flag to enable variable target thermostat thermostat choice of temperature control method to be used barostat choice of pressure control method to be used

BITOR bitorsions within the current structure

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

BNDPOT specifics of bond stretch functional forms

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

BOND covalent bonds in the current structure

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

BORDER bond orders for a conjugated pisystem

pbpl pi-bond orders for bonds in “planar” pisystem pnpl pi-bond orders for bonds in “nonplanar” pisystem

BOUND control of periodic boundary conditions

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

BOXES parameters for periodic boundary conditions

xbox length in Angs of a-axis of periodic box ybox length in Angs of b-axis of periodic box zbox length in Angs of c-axis of periodic box alpha angle in degrees between b- and c-axes of box beta angle in degrees between a- and c-axes of box gamma angle in degrees between a- and b-axes of box 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 recip reciprocal lattice vectors as matrix columns volbox volume in Ang**3 of the periodic box beta_sin sine of the beta periodic box angle beta_cos cosine of the beta periodic box angle gamma_sin sine of the gamma periodic box angle gamma_cos cosine of the gamma periodic box angle beta_term term used in generating triclinic box gamma_term term used in generating triclinic box orthogonal flag to mark periodic box as orthogonal monoclinic flag to mark periodic box as monoclinic triclinic flag to mark periodic box as triclinic octahedron flag to mark box as truncated octahedron spacegrp space group symbol for the unitcell type

CELL periodic boundaries using replicated cells

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 ncell total number of cell replicates for periodic boundaries icell offset along axes for each replicate periodic cell

CHARGE partial charges for the current structure

pchg magnitude of the partial charges (e-) 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 chglist partial charge site for each atom (0=no charge)

CHGPOT specifics of charge-charge functional form

dielec dielectric constant for electrostatic interactions 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

CHRONO timing statistics for the current program

cputim elapsed cpu time in seconds since start of program

COUPLE near-neighbor atom connectivity lists

maxn13 maximum number of atoms 1-3 connected to an atom maxn14 maximum number of atoms 1-4 connected to an atom maxn15 maximum number of atoms 1-5 connected to an atom n12 number of atoms directly bonded to each atom i12 atom numbers of atoms 1-2 connected to each atom n13 number of atoms in a 1-3 relation to each atom i13 atom numbers of atoms 1-3 connected to each atom n14 number of atoms in a 1-4 relation to each atom i14 atom numbers of atoms 1-4 connected to each atom n15 number of atoms in a 1-5 relation to each atom i15 atom numbers of atoms 1-5 connected to each atom

CUTOFF cutoff distances for energy interactions

vdwcut cutoff distance for van der Waals interactions chgcut cutoff distance for charge-charge interactions dplcut cutoff distance for dipole-dipole interactions mpolecut cutoff distance for atomic multipole interactions vdwtaper distance at which van der Waals 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 ewaldcut cutoff distance for direct space Ewald summation use_ewald logical flag governing use of Ewald summation term use_lights logical flag to use method of lights neighbors

DERIV Cartesian coordinate 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-orbital torsion Cartesian coordinate derivatives debt stretch-torsion Cartesian coordinate derivatives dett torsion-torsion Cartesian coordinate derivatives dev van der Waals 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 der 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 atom & bond dipoles for current structure

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

DISGEO distance geometry bounds and parameters

bnd distance geometry upper and lower bounds matrix vdwrad hard sphere radii for distance geometry atoms 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 use_invert flag to use enantiomer closest to input structure use_anneal flag to use simulated annealing refinement

DOMEGA 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-orbital torsion derivatives over torsions tebt stretch-torsion derivatives over torsions tett torsion-torsion derivatives over torsions tev van der Waals 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 ter 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

ENERGI 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-orbital torsion potential energy of the system ebt stretch-torsion potential energy of the system ett torsion-torsion potential energy of the system ev van der Waals 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 er 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 parameters for regular or PM Ewald summation

aewald Ewald convergence coefficient value (Ang-1) frecip fractional cutoff value for reciprocal sphere tinfoil flag governing use of tinfoil boundary conditions

EWREG exponential factors for regular Ewald sum

maxvec maximum number of k-vectors per reciprocal axis ejc exponental factors for cosine along the j-axis ejs exponental factors for sine along the j-axis ekc exponental factors for cosine along the k-axis eks exponental factors for sine along the k-axis elc exponental factors for cosine along the l-axis els exponental factors for sine along the l-axis

FACES variables for Connolly area and volume

maxnbr 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 maxep maximum number of convex edges maxfs maximum number of saddle faces maxcy maximum number of cycles mxcyep maximum number of cycle convex edges maxfp maximum number of convex faces mxfpcy maximum number of convex face cycles

FIELDS molecular mechanics force field description

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

FILES name and number of current structure files

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

FRACS atom 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

GROUP partitioning of system into atom groups

grpmass total mass of all the atoms in each group wgrp weight for each set of group-group interactions ngrp total number of atom groups in the system kgrp contiguous list of the atoms in each group igrp first and last atom of each group in the list grplist number of the group to which each atom belongs 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 cutoff value for Hessian matrix elements

hesscut magnitude of smallest allowed Hessian element

HESSN Cartesian Hessian elements for a single 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

IMPROP improper dihedrals in the current structure

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

IMPTOR improper torsions in the current structure

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 nitors total number of improper torsional angles in the system iitors numbers of the atoms in each improper torsional angle

INFORM control values for I/O and program flow

digits decimal places output for energy and coordinates iprint steps between status printing (0=no printing) iwrite steps between coordinate dumps (0=no dumps) isend steps between socket communication (0=no sockets) verbose logical flag to turn on extra information debug logical flag to turn on full debug printing holdup logical flag to wait for carriage return on exit abort logical flag to stop execution at next chance

INTER sum of intermolecular energy components

einter total intermolecular potential energy

IOUNIT Fortran input/output (I/O) unit numbers

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

KANANG forcefield parameters for angle-angle terms

anan angle-angle cross term parameters for each atom class

KANGS forcefield parameters for bond angle bending

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 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 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 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 kaf string of atom classes for Fourier angle bends

KATOMS forcefield parameters for the atom types

weight average atomic mass of each atom type 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 symbol modified atomic symbol for each atom type describe string identifing each of the atom types

KBONDS forcefield parameters for bond stretching

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 forcefield parameters for partial charges

chg partial charge parameters for each atom type

KDIPOL forcefield parameters for bond dipoles

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

KEYS contents of current keyword parameter file

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

KGEOMS parameters for the geometrical restraints

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 depth depth of shallow Gaussian basin restraint width exponential width coefficient of Gaussian basin rwall radius of spherical droplet boundary restraint npfix number of position restraints to be applied ipfix atom number involved in each position restraint kpfix flags to use x-, y-, z-coordinate position restraints ndfix number of distance restraints to be applied idfix atom numbers defining each distance restraint nafix number of angle restraints to be applied iafix atom numbers defining each angle restraint ntfix number of torsional restraints to be applied itfix atom numbers defining each torsional restraint ngfix number of group distance restraints to be applied igfix group numbers defining each group distance restraint nchir number of chirality restraints to be applied ichir atom numbers defining each chirality restraint use_basin logical flag governing use of Gaussian basin use_wall logical flag governing use of droplet boundary

KHBOND forcefield parameters for H-bonding terms

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 forcefield parameters for improper dihedral

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 forcefield parameters for improper torsions

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 forcefield parameters for atomic multipoles

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 forcefield parameters for out-of-plane bend

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

KOPDST forcefield parameters for out-plane distance

maxnopb maximum number of out-of-plane distance entries copb force constant parameters for out-of-plane distance kaopb string of atom classes for out-of-plane distance

KORBS forcefield parameters for pisystem orbitals

maxnpi maximum number of pisystem bond parameter entries electron number of pi-electrons for each atom class ionize ionization potential for each atom class repulse repulsion integral value for each atom class sslope slope for bond stretch vs. pi-bond order tslope slope for 2-fold torsion vs. pi-bond order kpi string of atom classes for pisystem bonds

KPITOR forcefield parameters for pi-orbit torsions

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

KPOLR forcefield parameters for polarizability

polr dipole polarizability parameters for each atom type pgrp connected types in polarization group of each atom type

KSTBND forcefield parameters for stretch-bending

stbn stretch-bending parameters for each atom class

KSTTOR forcefield parameters for stretch-torsions

maxnbt maximum number of stretch-torsion parameter entries btcon force constant parameters for stretch-torsion kbt string of atom classes for bonds in stretch-torsion

KTORSN forcefield parameters for torsional angles

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 forcefield parameters for torsion-torsions

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 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 tnx number of columns in torsion-torsion spline grid tny number of rows in torsion-torsion spline grid ktt string of torsion-torsion atom classes

KURYBR forcefield parameters for Urey-Bradley terms

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 forcefield parameters for special vdw terms

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 forcefield parameters for van der Waals terms

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

LIGHT indices for method of lights pair neighbors

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 pointer from x-sorted list into original interaction list locy pointer from y-sorted list into original interaction list locz pointer from z-sorted list into original interaction list rgx pointer from original interaction list into x-sorted list rgy pointer from original interaction list into y-sorted list rgz pointer from original interaction list into z-sorted list

LINMIN parameters for line search minimization

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

MATH mathematical and geometrical constants

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

MDSTUF control of molecular dynamics trajectory

nfree total number of degrees of freedom for a system velsave flag to save velocity vector components to a file frcsave flag to save force vector components to a file uindsave flag to save induced atomic dipoles to a file integrate type of molecular dynamics integration algorithm

MINIMA general parameters for minimizations

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

MOLCUL individual molecules within current system

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

MOLDYN velocity and acceleration on MD trajectory

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

MOMENT components of electric multipole moments

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 specifics of atomic multipole functions

m2scale factor by which 1-2 multipole interactions are scaled m3scale factor by which 1-3 multipole interactions are scaled m4scale factor by which 1-4 multipole interactions are scaled m5scale factor by which 1-5 multipole interactions are scaled

MPOLE multipole components for current structure

maxpole max components (monopole=1,dipole=4,quadrupole=13) pole multipole values for each site in the local frame rpole multipoles rotated to the global coordinate system npole total number of multipole sites in the system ipole number of the atom for each multipole site polsiz number of mutipole components at each multipole site zaxis number of the z-axis defining atom for each site xaxis number of the x-axis defining atom for each site yaxis number of the y-axis defining atom for each site polaxe local axis type for each multipole site

MUTANT hybrid atoms for free energy perturbation

lambda weighting of initial state in hybrid Hamiltonian nhybrid number of atoms mutated from initial to final state ihybrid 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 alter true if an atom is to be mutated, false otherwise

NUCLEO parameters for nucleic acid structure

bkbone phosphate backbone angles for each nucleotide glyco glycosidic torsional angle for each nucleotide pucker sugar pucker, either 2=2’-endo or 3=3’-endo 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 dihedrals for torsional space computations

dihed current value in radians of each dihedral angle 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

OPBEND out-of-plane bends in the current structure

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

OPDIST out-of-plane distances in current structure

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

ORBITS orbital energies for conjugated pisystem

q number of pi-electrons contributed by each atom w ionization potential of each pisystem atom em repulsion integral for each pisystem atom nfill number of filled pisystem molecular orbitals

OUTPUT control of coordinate output file format

archive logical flag to save structures in an archive noversion logical flag governing use of filename versions overwrite logical flag to overwrite intermediate files inplace cyclesave logical flag to mark use of numbered cycle files coordtype selects Cartesian, internal, rigid body or none

PARAMS contents of force field parameter file

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

PATHS parameters for Elber reaction path method

p0 reactant Cartesian coordinates as variables p1 product Cartesian coordinates as variables pmid midpoint between the reactant and product pvect vector connecting the reactant and product pstep step per cycle along reactant-product vector pzet current projection on reactant-product vector pnorm length of the reactant-product vector acoeff transformation matrix ‘A’ from Elber paper gc gradients of the path constraints

PDB definition of a Protein Data Bank structure

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 npdb number of atoms stored in Protein Data Bank format resnum number of the residue to which each atom belongs 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 pdbtyp Protein Data Bank record type assigned to each atom atmnam Protein Data Bank atom name assigned to each atom resnam Protein Data Bank residue name assigned to each atom

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

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

PIORBS conjugated system in the current structure

norbit total number of pisystem orbitals in the system iorbit numbers of the atoms containing pisystem orbitals reorbit number of evaluations between orbital updates piperp atoms defining a normal plane to each orbital nbpi total number of bonds affected by the pisystem bpi bond and piatom numbers for each pisystem bond ntpi total number of torsions affected by the pisystem tpi torsion and pibond numbers for each pisystem torsion listpi atom list indicating whether each atom has an orbital

PISTUF bonds and torsions in the current pisystem

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 pi-orbital torsions in the current structure

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

PME parameters for particle mesh Ewald summation

maxfft maximum number of points along each FFT direction maxorder maximum order of the B-spline approximation maxtable maximum size of the FFT table array maxgrid maximum dimension of the PME charge grid array 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 table intermediate array used by the FFT calculation nfft1 number of grid points along the a-axis direction nfft2 number of grid points along the b-axis direction nfft3 number of grid points along the c-axis direction bsorder order of the PME B-spline approximation

POLAR polarizabilities and induced dipole moments

polarity dipole polarizability for each multipole site (Ang**3) pdamp value of polarizability damping factor for each site uind induced dipole components at each multipole site uinp induced dipoles in field used for energy interactions npolar total number of polarizable sites in the system

POLGRP polarizable site 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 ip11 atom numbers of atoms in same group as each atom np12 number of atoms in groups 1-2 to each atom ip12 atom numbers of atoms in groups 1-2 to each atom np13 number of atoms in groups 1-3 to each atom ip13 atom numbers of atoms in groups 1-3 to each atom np14 number of atoms in groups 1-4 to each atom ip14 atom numbers of atoms in groups 1-4 to each atom

POLPOT specifics of polarization functional form

poleps induced dipole convergence criterion (rms Debyes/atom) polsor induced dipole SOR convergence acceleration factor pgamma prefactor in exponential polarization damping term p2scale field 1-2 scale factor for energy evaluations p3scale field 1-3 scale factor for energy evaluations p4scale field 1-4 scale factor for energy evaluations p5scale field 1-5 scale factor for energy evaluations d1scale field intra-group scale factor for direct induced d2scale field 1-2 group scale factor for direct induced d3scale field 1-3 group scale factor for direct induced d4scale field 1-4 group scale factor for direct induced u1scale field intra-group scale factor for mutual induced u2scale field 1-2 group scale factor for mutual induced u3scale field 1-3 group scale factor for mutual induced u4scale field 1-4 group scale factor for mutual induced poltyp type of polarization potential (direct or mutual)

POTENT usage of each potential energy component

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-orbital torsion term use_strtor logical flag governing use of stretch-torsion term use_tortor logical flag governing use of torsion-torsion term use_vdw logical flag governing use of vdw der Waals 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_rxnfld logical flag governing use of reaction field term use_solv logical flag governing use of surface area solvation use_gbsa logical flag governing use of GB/SA 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_orbit logical flag governing use of pisystem computation

PRECIS values of machine precision tolerances

tiny the smallest positive floating point value small the smallest relative floating point spacing huge the largest relative floating point spacing

REFER storage of reference atomic coordinate set

xref reference x-coordinate for each atom in the system yref reference y-coordinate for each atom in the system zref reference z-coordinate for each atom in the system nref total number of atoms in the reference system reftyp atom type for each atom in the reference system n12ref number of atoms bonded to each reference atom i12ref atom numbers of atoms 1-2 connected to each atom refleng length in characters of the reference filename refltitle length in characters of the reference title string refnam atom name for each atom in the reference system reffile base filename for the reference structure reftitle title used to describe the reference structure

RESDUE standard biopolymer residue abbreviations

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

RGDDYN velocities and momenta for rigid body MD

vcm current translational velocity of each rigid body wcm current angular velocity of each rigid body lm current angular momentum of each rigid body linear logical flag to mark group as linear or nonlinear

RIGID 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 number and location of small ring structures

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

ROTATE molecule partitions for rotation of a bond

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 reaction field matrix elements and indices

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

RXNPOT specifics of reaction field functional form

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 parameter scale factors for optimization

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

SEQUEN sequence information for a 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

SHAKE definition of Shake/Rattle constraints

krat ideal distance value for rattle constraint nrat number of rattle distance constraints to apply nratx number of atom group spatial constraints to apply irat atom numbers of atoms in a rattle constraint iratx group number of group in a spatial constraint kratx spatial constraint type (1=plane, 2=line, 3=point) ratimage flag to use minimum image for rattle constraint use_rattle logical flag to set use of rattle contraints

SHUNT polynomial switching function coefficients

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 parameter values to set array dimensions

“sizes.i” sets values for critical array dimensions used throughout the software; these parameters will fix the size of the largest systems that can be handled; values too large for the computer’s memory and/or swap space to accomodate will result in poor performance or outright failure

parameter: maximum allowed number of:

maxatm atoms in the molecular system maxval atoms directly bonded to an atom maxgrp user-defined groups of atoms maxtyp force field atom type definitions maxclass force field atom class definitions maxprm lines in the parameter file maxkey lines in the keyword file maxrot bonds for torsional rotation maxvar optimization variables (vector storage) maxopt optimization variables (matrix storage) maxhess off-diagonal Hessian elements maxlight sites for method of lights neighbors maxvib vibrational frequencies maxgeo distance geometry points maxcell unit cells in replicated crystal maxring 3-, 4-, or 5-membered rings maxfix geometric constraints and restraints maxbio biopolymer atom definitions maxres residues in the macromolecule maxamino amino acid residue types maxnuc nucleic acid residue types maxbnd covalent bonds in molecular system maxang bond angles in molecular system maxtors torsional angles in molecular system maxbitor bitorsions in molecular system maxpi atoms in conjugated pisystem maxpib covalent bonds involving pisystem maxpit torsional angles involving pisystem

SOCKET control parameters for socket communication

runtyp calculation type for passing socket information cstep current optimization or dynamics step number cdt current dynamics cumulative simulation time cenergy current potential energy from simulation cdx current gradient components along the x-axis cdy current gradient components along the y-axis cdz current gradient components along the z-axis skt_init logical flag set to true after socket initialization use_socket logical flag governing use of external sockets use_gui logical flag to show Tinker was invoked from GUI closing logical flag to indicate JVM and server shutdown

SOLUTE parameters for continuum solvation models

rsolv atomic radius of each atom for continuum solvation vsolv atomic volume of each atom for continuum solvation asolv atomic solvation parameters (kcal/mole/Ang**2) rborn Born radius of each atom for GB/SA solvation drb solvation derivatives with respect to Born radii doffset dielectric offset to continuum solvation atomic radii p1 single-atom scale factor for analytical Still GB/SA p2 1-2 interaction scale factor for analytical Still GB/SA p3 1-3 interaction scale factor for analytical Still GB/SA p4 nonbonded scale factor for analytical Still GB/SA p5 soft cutoff parameter for analytical Still GB/SA gpol polarization self-energy values for each atom shct overlap scaling factors for Hawkins-Cramer-Truhlar GB/SA 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 solvation model (ASP, SASA, ONION, STILL, HCT, ACE)

STODYN frictional coefficients for SD trajectory

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

STRBND stretch-bends in the current structure

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

STRTOR stretch-torsions in the current structure

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

SYNTRN definition of synchronous transit path

t value of the path coordinate (0=reactant, 1=product) pm 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

TITLES title for the current molecular system

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

TORPOT specifics of torsional functional forms

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-orbital torsion energy to kcal/mole storunit convert stretch-torsion energy to kcal/mole ttorunit convert stretch-torsion energy to kcal/mole

TORS torsional angles within the current structure

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 ntors total number of torsional angles in the system itors numbers of the atoms in each torsional angle

TORTOR torsion-torsions in the current structure

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

TREE potential smoothing & search tree levels

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

UNITS physical constants and unit conversions

avogadro Avogadro’s number (N) in particles/mole boltzmann Boltzmann constant (kB) in g*Ang**2/ps**2/K/mole gasconst ideal gas constant (R) in kcal/mole/K lightspd speed of light in vacuum (c) in cm/ps bohr conversion from Bohrs to Angstroms joule conversion from calories to joules evolt conversion from Hartree to electron-volts hartree conversion from Hartree to kcal/mole electric conversion from electron**2/Ang to kcal/mole debye conversion from electron-Ang to Debyes prescon conversion from kcal/mole/Ang**3 to Atm convert conversion from kcal to g*Ang**2/ps**2

UREY Urey-Bradley interactions in the structure

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

URYPOT specifics of Urey-Bradley functional form

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

USAGE atoms active during energy computation

nuse number of active atoms used in energy calculation use true if an atom is active, false if inactive

VDW van der Waals parameters for current structure

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 kred value of reduction factor parameter for each atom ired attached atom from which reduction factor is applied nvdw total number van der Waals active sites in the system ivdw number of the atom for each van der Waals active site

VDWPOT specifics of van der Waals functional form

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 igauss coefficients of Gaussian fit to vdw potential ngauss number of Gaussians used in fit to vdw potential 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

VIRIAL components of internal virial tensor

vir total internal virial Cartesian tensor components

WARP parameters for potential surface smoothing

m2 second moment of the GDA gaussian for each atom 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 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 crystal structures for parameter fitting

e0_lattice ideal lattice energy for the current crystal moment_0 ideal dipole moment for monomer from crystal nxtal number of crystal structures to be stored nvary number of potential parameters to optimize ivary index for the types of potential parameters vary atom numbers involved in potential parameters iresid crystal structure to which each residual refers rsdtyp experimental variable for each of the residuals vartyp type of potential parameter to be optimized

ZCLOSE ring openings and closures for Z-matrix

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

ZCOORD Z-matrix internal coordinate definitions

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 iz defining atom numbers for each Z-matrix atom