CHARMM Element doc/subst.doc $Revision: 1.5 $#File: SUBST, Node: Top, Up: (chmdoc/commands.doc), Next: Substition:(chmdoc/energy.doc), Previous: (chmdoc/commands.doc) Command Line Substitution ParametersThe following are substitution parameters available within CHARMM;---------------------------------------------------------------------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---------------------------------------------------------------------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' ----------------------------------------------------------------------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---------------------------------------------------------------------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 ---------------------------------------------------------------------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---------------------------------------------------------------------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---------------------------------------------------------------------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---------------------------------------------------------------------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---------------------------------------------------------------------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---------------------------------------------------------------------Shape analysis'SFIT' -'THET' -'XAXI' -'YAXI' -'ZAXI' -'RAXI' ----------------------------------------------------------------------Saddle point calculation (TRAVel)'SADE' - Saddle point energy'SADI' - Saddle point index'SADO' - Saddle point order---------------------------------------------------------------------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---------------------------------------------------------------------Minimization results:'MINCONVRG' -'MINECALLS' -'MINGRMS' -'MINSTEPS' ----------------------------------------------------------------------PERT results:'TPDEL' - Thermodynamic Perturbation energy change'TPTOT' - Thermodynamic