Command Line Substitution Parameters
The following are substitution parameters available within CHARMM;
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General:
'PI ' - Pi, 3.141592653589793
'KBLZ' - The Boltzmann factor (0.001987191)
'CCELEC' - 1/(4 PI epsilon) in AKMA units (332.0716)
'SPEEDL' - Speed of light
'CNVFRQ' - Conversion from root(Kcals/mol/AMU) to frequencies in CM-1.
'TIMFAC' - Conversion from AKMA time to picoseconds
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Control and system variables:
'BOMLEV' - The error termination level (-5 to 5)
'WRNLEV' - The warning print level (-5 to 10)
'PRNLEV' - The standard print level (-1 to 15)
'IOLEV' - The I/O level (-1 to 1)
'IOSTAT' - The status of most recent OPEN command (-1=failed,1=OK)
'TIMER' -
'FASTER' -
'LFAST' -
'OLMACH' -
'OUTU' -
'FLUSH' -
'FNBL' -
'NBFACT' -
'LMACH' -
'MYNODE' - Current node number (0 to NUMNODE-1)
'NUMNODE' - The number of nodes (distributed memory)
'NCPU' - The number of CPUs (shared memory use)
'SYSSTAT' -
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PSF counts
'NSEG' - Number of segments
'NRES' - Number of residues
'NATO' - Number of atoms
'NATOM' - "
'NGRP' - Number of groups
'NBON' - Number of bonds
'NBOND' - "
'NTHE' - Number of angles
'NTHETA' - "
'NPHI' - Number of dihedrals
'NIMP' - Number of improper dihedrals
'NIMPHI' - "
'NACC' - Number of acceptors
'NDON' - Number of donors
'NNB' - Number of explicit nonbond exclusions
'CGTOT' - Total system charge
'MASST' - Total system mass
'NATI' - Total number of image plus primary atoms
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Parameter counts
'NATC' - Number of atom types
'NCB' - Number of bond parameters
'NCT' - Number of angle parameters
'NCSB' - Number of stretch-bend parameters
'NCP' - Number of diheral parameters
'NCI' - Number of improper dihedral parameters
'NCOOP' - Number of out-of-plane parameters
'NCH' - Number of hydrogen bond parameters
'NCN' - Number of vdw parameter pairs
'NCQ' - Number of bond charge increments
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Other counts
'NCSP' - Number of restrained dihedral (CONS DIHE command).
'NTRA' - Number of image transformations
'TOTK' - Number of Ewald K vectors (not PME)
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Dimension Limits
'MAXA' - Number of atoms
'MAXATC' - Number of atom types
'MAXB' - Number of bonds
'MAXIMP' - Number of improper dihedrals
'MAXNB' - Number of explicit nonbond exclusions
'MAXP' - Number of dihedrals
'MAXPAD' - Number of donors and acceptors
'MAXRES' - Number of residues
'MAXSEG' - Number of segments
'MAXT' - Number of angles
'MAXCB' - Number of bond parameters
'MAXCH' - Number of hydrogen bond parameters
'MAXCI' - Number of improper dihedral parameters
'MAXCN' - Number of vdw pair parameters
'MAXCP' - Number of dihedral parameters
'MAXCT' - Number of angle parameters
'MAXCSP' - Number of restrained dihedrals
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Coordinate manipulation parameters:
'XAXI' - vector and length of defined axis (COOR AXIS command).
'YAXI'
'ZAXI'
'RAXI'
'XCEN' - origin of axis vector
'YCEN'
'ZCEN'
'XMIN' - Extreme values (COOR STAT command)
'YMIN'
'ZMIN'
'WMIN'
'XMAX'
'YMAX'
'ZMAX'
'WMAX'
'XAVE' - Average values (COOR STAT command).
'YAVE'
'ZAVE'
'WAVE'
'MASS' - mass of selected atoms
'RMS' - Root mean squared difference between two structures.
'MASS' - mass (COOR ORIE and COOR RMS commands).
'XMOV' - displacement of atoms from best fit (COOR ORIE command).
'YMOV' -
'ZMOV' -
'XCEN' -
'YCEN' -
'ZCEN' -
'THET' - Angle of rotation from best fit
'AREA' - Requested surface area (COOR SURF command).
'VOLUME' - Requested volume (COOR VOLUme command).
'NVAC' - Number of vacuum points
'NOCC' - Number of occupied points
'NSEL' - Number of selected points
'FREEVOL'- Total free volume
'MIND' - Minimum distance (COOR MIND command).
'NPAIR' - Number of pairs (COOR DIST command).
'NCONTACT' - Number of contacts (COOR DMAT command).
'RGYR' - Radius of gyration (COOR RGYR command).
'XCM' - Center of mass (COOR RGYR command).
'YCM' -
'ZCM' -
'MASS' - Mass of selected atoms
'XDIP' - Dipole moment (COOR DIPOle command)
'YDIP' -
'ZDIP' -
'MDIP' - Dipole magnitude
'CHARGE'- Charge of selected atoms
'NHBOND' - total number of hydrogen bonds (COOR HBONd command).
'AVNOHB' - Average number of hydrogen bonds
'AVHBLF' - Average hydrogen bond life
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SCALar STATistics command substitution parameters:
'SMIN' - Minimum value
'SMAX' - Maximum value
'SAVE' - Average value
'SVAR' - Variance about average
'SWEI' - Total weight used in the averaging
'STOT' - Total of selected atoms
'NSEL' - Number of selected atoms
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Quick command substitution paramteters:
'XVAL' - X position of group of atoms
'YVAL' - X position of group of atoms
'ZVAL' - X position of group of atoms
'DIST' - Distance between two atom analysis
'THET' - Angle for three atom analysis
'PHI ' - Dihedral for four atom analysis
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Shape analysis
'SFIT' -
'THET' -
'XAXI' -
'YAXI' -
'ZAXI' -
'RAXI' -
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Saddle point calculation (TRAVel)
'SADE' - Saddle point energy
'SADI' - Saddle point index
'SADO' - Saddle point order
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Energy calculation results:
'XCM' - Center of mass (from MMFP energy term calcuation)
'YCM' -
'ZCM' -
'XCM2' - Spatial extent
'YCM2' -
'ZCM2' -
'RGEO' - average distance from reference
'ENPB' - electrostatic free energy of solvation (from PBEQ)
'RMAX' - maximum distance to origin for the SSBP energy term
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Minimization results:
'MINCONVRG' -
'MINECALLS' -
'MINGRMS' -
'MINSTEPS' -
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PERT results:
'TPDEL' - Thermodynamic Perturbation energy change
'TPTOT' - Thermodynamic Perturbation total energy
'TIDEL' - Thermodynamic Integration energy change
'TITOT' - Thermodynamic Integration total energy
'SLDEL' - Slow Growth energy change
'SLTOT' - Slow Growth total energy
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Atom selection parameters:
'NSEL' - Number of selected atoms from the most recent atom selection.
'SELATOM' - Atom number of first selected atom
'SELCHEM' - Chemical type of first selected atom
'SELIRES' - Residue number of first selected atom
'SELISEG' - Segment number of first selected atom
'SELRESI' - Resid of first selected atom
'SELRESN' - Residue type of first selected atom
'SELSEGI' - Segid of first selected atom
'SELTYPE' - Atom name of first selected atom
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Crystal parameters
'XTLA' - Unit cell dimensions
'XTLB' -
'XTLC' -
'XTLALPHA' - Unit cell angles
'XTLBETA' -
'XTLGAMMA' -
'XTLXDIM' - Number of crystal degrees of freedom (cube=1,triclinic=6,..)
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Nonbond list counts
'NNBA' - Number of atom pairs (main list)
'NNBG' - Number of group pairs (main list)
'NNBI' - Number of crystal atom pairs (Phonons only)
'NRXA' - Number of atom exclusions due to replicas
'NRXG' - Number of group exclusions due to replicas
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Correlation Function Results
'AVER' - Series average (CORREL's SHOW command)
'FLUC' - Series fluctuation
'P2' - P2 average
'P2R3' -
'P2RA' -
'R3R' -
'R3S' -
'P0' - Polynomial best fit components (MANTime POLY command).
'P1' -
'P2' -
'P3' -
'P4' -
'P5' -
'P6' -
'P7' -
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Vibrational analysis of thermodynamic properties:
'FTOT' - Vibrational free energy.
'STOT' - Vibrational entropy.
'HTOT' - Vibrational enthalpy.
'CTOT' - Vibrational heat capacity.
'ZTOT' - Zero point correction energy.
'FCTO' - Classical vibrational free energy.
'ETOT' - Total harmonic limit classical free energy
(to compare with free energy perturbation simulations).
'TRAC' - Trace of the Hessian for selected atoms
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Miscellaneous:
'VIOL' - Total violation for all NOE restraints (NOE WRITe/PRINt ANAL)
'DRSH' - the DRSH value in subroutine PSHEL (undocumented)
(also undocumented in fcm/mmfp.fcm in violation of coding stds.)
'DCOEFF'- The diffusion constant (COOR ANALysis SOLVent command).
'TIME' - simulation time(ps) for current frame in trajectory reading
'STEP' - Step number for current frame in trajectory reading
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See energy.doc for the energy related substitution parameters.
NIH/NHLBI/LBC Computational Biophysics Section
FDA/CBER/OVRR Laboratory of Biophysics