Feig at 21:23, 11 August 2006

2006-08-11T21:23:05Z

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__NOTOC__
== Usage ==

<mmtsbToolUsage cmd="mdCHARMM.pl"></mmtsbToolUsage>

== Description ==

This script allows running molecular dynamics simulations with CHARMM.
It is intended primarily for running protein simulations with implicit solvent
in the NVT ensemble.
Particle Mesh Ewald electrostatics, Langevin dynamics, periodic boundaries,
NPT ensembles and other more advanced simulation features are not supported at this
point but may be added in the future. 
Simulation parameters are set with -par. A list of available parameters is
given <A HREF="http://mmtsb.scripps.edu/cgi-bin/charmmpar" TARGET=cpar>here</A>.
Various restraints can be set with -l, -cons, and -hmcm
as in <docmark>minCHARMM.pl</docmark> 
The remaining options are used to set input and output files. With -stdout
a common tag may be given to generate the standard set of output files.
To set file names individual files the options -enerout, -trajout,
-restout, -final, -elog, -log, -cmd are available
for the trajectory output file, the restart output file, a PDB file with the
final conformation, an energy log file, a CHARMM log file, and commands sent to CHARMM,
respectively. 
The option -restart is available to restart a simulation from a
previously written restart file.

== Options ==

; -help : usage information

== Examples ==

<mmtsbToolExample cmd="mdCHARMM.pl" set="/apps/mmtsb/bench/mdCHARMM.pl-test/test1"></mmtsbToolExample>

<mmtsbToolExample cmd="mdCHARMM.pl" set="/apps/mmtsb/bench/mdCHARMM.pl-test/test2"></mmtsbToolExample>

<mmtsbToolExample cmd="mdCHARMM.pl" set="/apps/mmtsb/bench/mdCHARMM.pl-test/test3"></mmtsbToolExample>

MdCHARMM.pl - Revision history

Feig at 21:23, 11 August 2006