[gmx-users] How to run GROMACS in cluster

[Justin Lemkul]

On 11/1/19 7:40 AM, Shradheya R.R. Gupta wrote:
> Respected Researchers,
>
> I am trying to run GROMACS in parallel. So I have established connection
> using ssh, nfs and openmpi.
>
> The connection is working fine as I have run Autodock Vina-MPI and other
> test files.
>
> I have installed the GROMACS in the mounted directory which is shared by
> all the computers (not in individual computer).
>
> When I run GROMACS in parallel it is showing 10 minutes for 10ps and when
> run on single computer it is showing 5 minutes.
>
> How to resolve this issue?

Without knowing how GROMACS was installed, what your mdrun commands 
were, and the contents of the relevant .log files, no one can provide 
you any insight here. It may also be worth consulting your sysadmin for 
advice specific to your cluster.

-Justin

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Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
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jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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