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Gromacs is a versatile package to perform molecular dynamics

Version: 4.5.5

  • MachinesClusters: ember, updraft & sanddunearch
  • Location/Directory:
    • ember: /uufs/ember.arches/sys/pkg/gromacs/4.5.5{d,f}_mvapich2-1.7i
    • updraft:/uufs/updraft.arches/sys/pkg/gromacs/4.5.5{d,f}_mvapich2-1.7i
    • sanddunearch:/uufs/sanddunearch.arches/sys/pkg/gromacs/4.5.5{d,f}_mvapich2-1.7i
    One must choose either the suffix d or f. The invocation of the d suffix implies that one uses an FFT the gromacs package uses the Fast Fourier Transform (FFT) with double precision; the invocation of the 
    f suffix implies the use of a single precision FFT.

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 the package.

To Use:

Each cluster (ember/updraft/sanddunearch) has its own gromacs executables (stored in the aforementioned directorydirectories

because these executables were each executable was compiled with a cluster specific MPI library (mvapich2 v1.7)

The following sample scripts can be used on:

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.

No Format
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 4						<-- enter processors per node, in agreement with #PBS line