Re: Reading from DCD file and running MD

From: Jérôme Hénin (
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.


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

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