RE: Fw: Re: Re: How to read trajectory within CHARMM generated by NAMD

From: David A. Horita (dhorita_at_wfubmc.edu)
Date: Mon Dec 28 2009 - 08:33:31 CST

charmm and namd dcd and psf files are close but not identical. The psf, in particular, is problematic because charmm uses atom type numbers while namd uses names. There are a variety of ways to convert back and forth (google charmm namd psf). The main thing to watch for is that the atom ordering is the same. The psfgen routine can write both namd and charmm formats (writepsf charmm name.psf) - so you can have charmm and namd format psf's at the outset.

dcd files are similar but namd doesn't default to writing data into certain header fields. this will matter if you're merging several namd trajectories because charmm will keep reinitializing its counters and merge doesn't work properly. You can either read/write (in charmm), modify the headers with some programs in the source tree (not the binary distribution) of namd (dumpdcd.c, loaddcd.c, fixdcd.c) or combine the files in vmd and write a single trajectory - you can get charmm header information with google, as well as other methods to analyze multipart namd dcd's in charmm. Note that timestep is in AKMA units (and in my sims ok).

As Axel has noted (here and in other threads), try a simple, quick simulation (maybe run apoAI a bit longer than the benchmark) and figure out how to extract the information you want from that.

Regards,
Dave

-----------------------------
David A. Horita, Ph.D.
Department of Biochemistry
Wake Forest University School of Medicine
Winston-Salem, NC 27157-1016
Tel: 336 713-4194
Fax: 336 716-7671
email: dhorita_at_wfubmc.edu
web: http://www1.wfubmc.edu/biochem/faculty/Horita.htm

-----Original Message-----
From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On Behalf Of Axel Kohlmeyer
Sent: Monday, December 28, 2009 3:47 AM
To: Yang MIngjun
Cc: namd-l
Subject: Re: Fw: Re: Re: namd-l: How to read trajectory within CHARMM generated by NAMD

On Sun, Dec 27, 2009 at 9:06 PM, Yang MIngjun <yangzch_at_mail.ustc.edu.cn> wrote:
> Dear Axel,
>   Thanks for your response. I am not sure whether the .psf, .dcd files used in NAMD is compatible with the ones used in CHARMM. If so, then the .dcd files generated by NAMD can be analyzed by CHARMM (a package we used frequently here).  Is it possible for CHARMM to read in the two files?

how should i know??
_i_ don't use CHARMM.

if you have CHARMM available,
why don't you just try it?

axel

> Many thanks.
> Mingjun
>
>

-- 
Dr. Axel Kohlmeyer    akohlmey_at_gmail.com
Institute for Computational Molecular Science College of Science and Technology Temple University, Philadelphia PA, USA.

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