MMTSB
Tool Set Documentation

Difference between revisions of "mdNAMD.pl"

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Line 10: Line 10:
  
 
; -help : usage information
 
; -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 ==
 
== Examples ==

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]

Show source


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

Examples