Re: How to read trajectory within CHARMM generated by NAMD

From: Dimitar V Pachov (dpachov_at_brandeis.edu)
Date: Mon Dec 28 2009 - 11:52:59 CST

----- gaillard_at_chimie.u-strasbg.fr wrote:

| From: gaillard_at_chimie.u-strasbg.fr
| To: "Yang MIngjun" <yangzch_at_mail.ustc.edu.cn>
| Cc: "namd-l" <namd-l_at_ks.uiuc.edu>
| Sent: Monday, December 28, 2009 9:44:16 AM GMT -05:00 US/Canada Eastern
| Subject: Re: namd-l: How to read trajectory within CHARMM generated by NAMD
|
| Yang MIngjun <yangzch_at_mail.ustc.edu.cn> a écrit :
| > 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.

And 4) differences in how NAMD writes unit cell data for each frame. This is a crucial component if the DCD file is going to be used for CHARMM analysis involving energies and/or image manipulations. NAMD DCD files can be used AS IS for CHARMM analysis if ONLY primary cell geometrical properties are desired. Otherwise, correction of the cell data per frame should be made beforehand.

|
| 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

-- 
========================================================
Dimitar V Pachov
PhD Candidate
Physics & Biochemistry Department     Phone: (781) 736-2326
Brandeis University, MS 057           Email: dpachov_at_brandeis.edu
========================================================

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:51:50 CST