Gromacs is a versatile package to perform molecular dynamics

Version: 3.3.3

• Machines: Arches clusters
• Location:
  • arches: /uufs/arches/sys/pkg/gromacs/std

The home page for Gromacs is http://www.gromacs.org/. At this site you will find a summary of the program's capabilities along with documentation on how to use package.

To Use:

Arches PBS Script

The PBS script may be obtained here: gromacs.script

there are a number of variable to be set; the mdrun has a parallel version. The script here is for only the parallel version as all the nodes on arches have multiple processors. To run on one node just used NODES 1 and the proper PPN for the nodes requested.

setenv WORKDIR $HOME/gromacs/test/gromacs_sample	<-- enter the path to location of the input files
setenv SCRFLAG serial					<-- enter the scratch system (serial, serial-pio, mm, da)
setenv INMDP  md.mdp					<-- enter appropriate input file names
setenv INCRD  apo_pr.gro				<-- enter appropriate input file names
setenv INPRM  apo_ion.top				<-- enter appropriate input file names
setenv INNDX  apo.ndx					<-- enter appropriate input file names
setenv DEFFNM  apo_md					<-- enter appropriate input file names
setenv NODES 2						<-- enter number of nodes, in agreement with #PBS line
setenv PPN 2						<-- enter processors per node, in agreement with #PBS line