Difference between revisions of "mdNAMD.pl"

Revision as of 01:28, 1 August 2009

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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Description

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

@@ Line 10: / Line 10: @@
 ; -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
 == Examples ==