How about making a shell script and submitting the script instead?
Gustavo.
On Tuesday, June 15, 2010, vaibhav dixit wrote:
> Dear Amber community members,
>
> I'm running MD simulations on a set of proteins (72 pdb structures known for
> my target).
>
> Here I use procedure given in tutorial
> http://ambermd.org/tutorials/advanced/tutorial3/section1.htm
> to run min.in,
> heat.in, density.in and equil.in jobs one after the other on cluster through
> portal that we have here. Followed by production phase of the calculation.
>
> Is there any possibility where I can modify the input so that all these jobs
> will run one after the other (like link jobs) instead having to submit
> them separately?
>
> One issue is that the portal is adding some extra numbers in the last line
> of the restart file, which I have to remove manually before submitting the
> next job, else the job fails. Will this fact affect any such attempts to
> link these jobs?
>
> This linking of jobs will save time once prmtop and inpcrd files are
> prepared from the pdb.
>
> Please find time and see if you can suggest some solution for the same.
>
> Thank you all in advance and waiting for reply...
>
> --
> With regards
>
> Vaibhav A. Dixit
> Ph.D. Scholar
> Department of Medicinal Chemistry
> Natl. Inst. Pharm. Edu. & Res. (NIPER)
> Sector 67, Phase X, S.A.S. Nagar (Mohali)
> Punjab -160 062 INDIA
> Phone (Mobile): +919915214408
> E-mail: vaibhavadixit.gmail.com
> www.niper.nic.in
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Gustavo Seabra
Professor Adjunto
Departamento de Química Fundamental
Universidade Federal de Pernambuco
Fone: +55-81-2126-7417
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Jun 15 2010 - 04:30:03 PDT
