Re: how to convert dcd files from namd to charmm

From: Alessandro Cembran (
Date: Thu Mar 15 2007 - 07:59:01 CDT


I've been running NAMD and post processing the trajectories with CHARMM
as well and I've never run into any problem.
In some cases, one might have to pay attention to the orientation of the
box (I am thinking about hexagonal cells, that need to be rotated by 15
degrees around the Z axis) but the raw numbers are always read correctly.
Another thing that I can think of is that you might have run NAMD on a
computer of different endianness of the computer on which you are
analyzing the trajectory. If this is the case, you might
a) Recompile CHARMM with TESTENDIAN in the pref.dat (never tried this one)
b) Change the endianness of the shell on which you are running CHARMM to
match the original one:
    export F_UFMTENDIAN=little or ...=big
c) Compile and run CHARMM on the machine the trajectories have been

If none of the two cases applies to your problem, then could you be
more specific about what is the compatibility issue?

Alessandro wrote:
> Hello,
> I have done a simulation of a protein with NAMD, using the Charmm
> force field, and now I would like to perform an analysis with CHARMM.
> I have problems of compatibility of the trajectory files obtained
> with NAMD and CHARMM. Does anyboy knows how to convert a dcd
> trajectory file from NAMD to the correct one used by Charmm?
> Thanks a lot!
> Rebeca García
> Post-doctoral student
> Barcelona
> Spain

Alessandro Cembran,PhD
Post Doctoral Associate
Mailing Address:
Univ. of Minnesota, Dept. of Chemistry
G2, 139 Smith Hall 207 Pleasant St SE
Minneapolis, MN 55455-0431
Univ. of Minnesota, Walter Library
117 Pleasant St SE, Room 473
Phone: +1 612-624-4617

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:20:05 CST