From: Jérôme Hénin (jerome.henin_at_uhp-nancy.fr)
Date: Wed Dec 07 2005 - 16:19:08 CST
Hi Shahid,
How about a script that would:
* generate 20 NAMD config files from a template (using sed)
* invoke VMD with a small Tcl script that reads the DCD and writes one NAMD
binary coordinate file for each frame
* run NAMD with each config file
This way, you can run all the simulations in parallel on a cluster.
If you need help on how to perform any of these steps, many people on the list
(including myself) can help you.
If you specifically need to do that in a single NAMD job, it may still be
possible, but it probably won't be as flexible.
Best,
Jerome
Le Mercredi 07 Décembre 2005 21:35, Shahid Qamar a écrit :
> Hi,
> I have a dcd file which has 20 frames and I want to run MD for each fram in
> a wayn that it read first fram and run MD and then 2nd fram and run MD and
> so on. If anyone of you have any script or any idea then please help me
> out.
>
> Thanks in advance.
>
>
> Regards
-- Jérôme Hénin Equipe de Dynamique des Assemblages Membranaires Université Henri Poincaré / CNRS Tel : (33) 3 83 68 43 91 Fax : (33) 3 83 68 43 71 http://www.edam.uhp-nancy.fr/
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