Re: velocities from a DCD file

From: Axel Kohlmeyer (
Date: Wed Jan 27 2010 - 08:46:28 CST

On Wed, 2010-01-27 at 11:01 -0300, Raul Araya wrote:
> Dear NAMD users:
> I was trying to restart an old simulation but due to some storage
> problems at mi facility I lost the .vel and the .xsc restart files. I
> want to know if there is some way to obtain the velocities at the last
> frame and the periodic cell dimensions from the DCD trajectory file?

the velocities are really not that important. they are - of course -
_not_ stored in the position dcd file. you can approximate them from
finite differences, though.

cell dimensions may or may not be stored in the dcd file.
that depends on which version of NAMD you used and which


> Thanks...
> Raúl Araya Secchi
> B.Sc Molecular Biotechnology.
> Molecular Biotechnology Engineer.
> Centre for Bioinformatics CBUC,
> Faculty of Biological Sciences, P. Universidad Catolica de Chile
> Portugal # 49 – ZIP 6513492 Santiago – Chile Phone: + 56 2 6862269;

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

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