Re: How to read trajectory within CHARMM generated by NAMD

From: gaillard_at_chimie.u-strasbg.fr
Date: Mon Dec 28 2009 - 08:44:16 CST

Yang MIngjun <yangzch_at_mail.ustc.edu.cn> a crit:
> Dear all,
>
> We performed a MD simulation using NAMD with CHARMM force field.
> Now we are going to analyze the trajectory within CHARMM package.
> Would some one please tell me how to do this?
> Many thanks.
>
> Mingjun

Hi Mingjun,

Problems when exploiting NAMD trajectories with CHARMM can arise from
1) PSF compatibility issues (NAMD works with X-PLOR PSF format), 2)
slight differences in the DCD format (in the header part), 3)
endianness problems, etc.

To solve 1) you have to generate the PSF at the beginning of your
project with the CHARMM program and write it in both CHARMM and XPLOR
versions. The catdcd and flipdcd programs can help you solve 2) and 3).

Have a look at these threads on the CHARMM forum:

http://www.charmm.org/ubbthreads-7-5-3/ubbthreads.php?ubb=showflat&Number=16279
http://www.charmm.org/ubbthreads-7-5-3/ubbthreads.php?ubb=showflat&Number=22096

--
Thomas Gaillard
Laboratoire de Biochimie
Ecole Polytechnique
91128 Palaiseau, France

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