Re: catdcd-generated files and CHARMM

From: Mauricio Carrillo Tripp (
Date: Thu Jul 21 2005 - 14:05:10 CDT

I've found that the best way to deal with these issues is to use the merge
command from charmm itself, instead of using catdcd,
and I haven't had any problems since then... BTW, I also 1) make the psf
(xplor format) with charmm, then 2) run the simulation with
namd, and 3) go back to charmm to analysis, but I don't know if the first
step would make any difference in the third one.
So far, this approach has worked for me.

On 7/21/05, Chang, Christopher <> wrote:
> Hi,
> I'm trying to use the quasiharmonic analysis facility of CHARMM to analyze
> a trajectory created from multiple NAMD runs, then put together with the
> catdcd utility. Although the number of coordinate sets in the file is being
> seen correctly, I'm getting some other fishy output: "Time step was
> 0.000000 AKMA time units.", as well as a string of binary characters in
> what CHARMM interprets as the TITLE section of the DCD file.
> Are NAMD DCD files compatible with CHARMM, and if so does the catdcd
> utility to anyone's knowledge preserve this compatibility?
> Thanks,
> Chris
> Christopher H. Chang, Ph.D.
> Research Associate
> National Renewable Energy Laboratory
> 1617 Cole Blvd., Mail Stop 1608
> Golden, CO 80401
> Phone (303) 275-3751
> Fax (303) 275-4007

Mauricio Carrillo Tripp, PhD
Department of Chemistry
Wabash College

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