AMBER Archive (2008)

Subject: RE: AMBER: Restart MD Simulation

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Fri May 23 2008 - 17:28:16 CDT

This message really doesn't contain any information for us to be able to
help you. You could start by explaining what you mean by "unable to get it
running". What error messages do you see? What is behavior you are referring
to when you say "running"? Does it restart from the beginning? Does the
queuing system refuse to accept it as a valid job? Does it start running and
then crash with an error message? Is the server still broken?

You need to be much more explicit here.

> -----Original Message-----
> From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
> Of dpandit_at_brandeis.edu
> Sent: Friday, May 23, 2008 2:56 PM
> To: amber_at_scripps.edu
> Subject: AMBER: Restart MD Simulation
>
> Hi:
> I am using following script to restart my job which was aborted due to
> server failure but I am unable to get it running. I am using restart
> file but I am not sure what am I doing wrong?
>
> Thank you.
> Deepa
>
>
> #!/bin/bash
> #$ -S /bin/bash
> #$ -N pro_hGH_May23
> #$ -pe mpich 8
> #$ -M dpandit_at_brandeis.edu
> #$ -m bes
> mpirun -np 8 /share/apps/amber9/exe/sander.MPI -O -i pro_hGH_apr21.in
> -p hgh_sol_apr7.prmtop -c pro_hGH_5.rst -r pro_hGH_5_rst.rst -o
> pro_hGH_5_rst.out -x pro_hGH_5_rst.mdcrd
> gzip -9 pro_hGH_5_rst.mdcrd
> echo "DONE"
>
>
>
>
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