CHARMM c30b1 subst.doc



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                  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)
'NIC'     - Number of Internal Coordinate entries in the IC table

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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'  -
'RDIP'  - 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

'NHYDRR' - Average number of solvent molecule -solute contacts (COOR ANALys)
'NHYDAR' - Average number of solvent atom  - solute contacts (COOR ANALys)
'NHYDAA' - Average number of solvent atom -solute atom contacts (COOR ANALys)

'ENTROPY' - Configurational entropy estimate (COOR COVA THERmo)
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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
'DFLC'    - DIFFLC, ie the fluctuation about the average energy difference
'AVKE'    - Average kinetic energy
'KEFL'    - Fluctuation in kinetic 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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Data from most recently read (or current) trajectory file

'NFILE' - Number of frames in the trajectory file
'START' - Step number for the first frame
'SKIP'  - Frequency at which frames were saved
            (NSTEP=NFILE*SKIP when not using restart files)
'NSTEP' - Total number of steps in the simulation
'NDEGF' - Number of degrees of freedom in the simulation
            (Can be use to get the temperature with velocity files).
'DELTA' - The dynamics step length (in picoseconds).

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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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Generalized Born Solvation Calculation Results

'GBAL' - Generalized Born alpha values
'GBAT' - Generalized Born atomic solvation energy contributions values
'SIGX' - Partial contribution to GB force, X-direction (diagnostic)
'SIGY' - Partial contribution to GB force, Y-direction (diagnostic)
'SIGZ' - Partial contribution to GB force, Z-direction (diagnostic)
'T_GB' - Partial contribution to GB force, 3-body term (diagnostic)

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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
'PQRES' - Final value of target function in RMSDyn 2D-projection
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pref.dat Keywords:

The following keywords have substitutions of 0 or 1 for set or not-set,
respectively.

ACE       FOURD     MOLVIB  	OLDDYN    PNOE     RXNCOR   
ADUMB     GAMESS    MPI     	PARAFULL  POLAR    SCALAR   
ASPENER   GENBORN   MTS     	PARALLEL  PRIMSH   SHAPES   
BLOCK     GENCOMM   MULTCAN 	PARASCAL  PVM      SINGLE   
CFF       GENETIC   NIH     	PARVECT   PVMC     SOCKET   
CMPI      IMCUBES   NOCORREL	PATHINT   QHMCM    SOFTVDW  
CRAYVEC   LATTICE   NOIMAGES	PBEQ      QTSM     TNPACK   
DIMB      LDM       NOMISC  	PBOUND    QUANTA   TRAVEL   
DMCONS    LONEPAIR  NOST2   	PBOUNDC   QUANTUM  VECTOR   
DOCK      MC        NOVIBRAN	PERT      REPLICA  
EISPACK   MCSS      NO_BYCC 	PM1       RGYCONS  
FMA       MMFF      NO_BYCU 	PMEPLSM   RISM     

Example: In this case GENBORN keyword was in the pref.dat so
         ?genborn is substituted with 1 and the IF test will 
         evaluate as true.

 	  if ?genborn .eq. 1 then goto dogenborn
 
	   CHARMM>    if ?genborn .eq. 1 then goto dogenborn
 	   RDCMND substituted energy or value "?GENBORN" to "1"
 	   Comparing "1" and "1".
 	   IF test evaluated as true.  Performing command



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See energy.doc for the energy related substitution parameters.

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