catdcd-generated files and CHARMM

From: Chang, Christopher (Christopher_Chang_at_nrel.gov)
Date: Thu Jul 21 2005 - 11:55:25 CDT

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

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