[gmx-users] Script to submit the md simulations on cluster.

[Mark Abraham]

Hi,

No, we can't. Every cluster is set up differently. You have to consult your
local documentation and sysadmins. That said, shell scripts tend to prefer

NAME=value

ie without spaces

Mark

On Mon, Aug 24, 2015 at 7:28 AM Seera Suryanarayana <palusoori at gmail.com>
wrote:

> Dear gromacs users,
>
> I would like to submit the mdrun on cluster. I have written a shell script
> for submission as following.
>
> EXECUTABLE=./mdrun_mpi465
> ARGUMENTS = -v -deffnm md_0_1.tpr
> INPUT_FILES = file:///home/suryanarayana1599/md.mdp,
> file:///home/suryanarayana1599/npt.cpt,
> file:///home/suryanarayana1599/npt.gro,
> file:///home/suryanarayana1599/md_0_1.tpr,
> file:///home/suryanarayana1599/topol.top
> OUTPUT_FILES = md_0_1.trr,md_0_1.xtc,md_0_1.cpt
> STDIN_FILE = /dev/null
> STDOUT_FILE = ${JOB_ID}.out
> STDERR_FILE = ${JOB_ID}.err
> REQUIREMENTS = HOSTNAME="ggblr.garudaindia.in"(this is cluster name)
> TYPE="mpi"
> NP = 10
> OUTPUT_FILES = 2000
>
> Could any one tell me that whether the script is right.
>
> Thanks in Advance
>
> Surya
> Graduate student
> India.
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