mdNAMD.pl

Usage

usage:    mdNAMD.pl [options] PSFfile PDBfile
options:  [-restout tag] [-restart tag] [-final pdb] [-trajout DCDname]
          [-coor file] [-ext file]
          [-elog file] [-log file] [-cmd file]
          [-par NAMDparams] [-first step]
          [-custom file]
          [-consref file]

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Options

-help 

usage information

-restout tag 

write restart files (coor, vel, xsc)

-restart tag 

read restart files (coor, vel, xsc)

-final pdbname 

write final conformation in PDB format

-trajout DCDname 

write trajectory in DCD format

-coor file 

read input conformation from NAMD coor file

-ext file 

read box information from NAMD xsc file

-elog file 

write NAMD energy log file

-log file 

write NAMD log file

-cmd file 

write NAMD input script

-par key=value[,...] 

NAMD simulation parameters

-first step 

number of first time step

-custom file 

custom input file to be added to NAMD input file

-consref file 

provide PDB file to be used as reference for harmonic restraints