MMTSB
Tool Set Documentation

mdNAMD.pl

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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

This script interfaces with NAMD to run MD simulations. The usage is similar to mdCHARMM.pl and mdAmber.pl. NAMD offers only limited functionality compared to CHARMM but is faster, especially on parallel architectures.

NAMD needs to be installed and the environment variable NAMDEXEC needs to be set to the namd executable. For a parallel run, NAMDEXEC can be set for example as follows (MPI versions will require a different command):

setenv NAMDEXEC "/apps/namd/namd2.6x64/charmrun ++nodelist nodelist +p48 /apps/namd/namd2.6x64/namd2 +giga"

In this case, namd is installed under /apps/namd. The nodelist file has the following format:

group main
host snoopy
host snoopy
host scoobydoo
host scoobydoo
host scoobydoo
...

You may also have to specify to use ssh instead of rsh:

setenv CONV_RSH ssh

NAMD requires a PDB and a PSF file as input. The PSF file can be generated using CHARMM (with genPSF.pl using the -xplor option).

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

mdNAMD.pl -par dynsteps=500,boxsize=41.1779,dyntemp=300,minsteps=100 -restout run1 -log run1.out cpeptide.psf cpeptide.solvated.pdb


carries out a short MD run with NAMD after initial minimization


mdNAMD.pl -par dynsteps=2000,dynoutfrq=100 -restart run1 -restout run2 -trajout run2.dcd -log run2.out cpeptide.psf cpeptide.solvated.pdb


continues a previous run for another 2000 steps, writing out conformations every 100 steps to a DCD trajectory file.