Re: velocities from a DCD file

From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Wed Jan 27 2010 - 09:08:52 CST

Hi Raul,

There is no way to recover the instantaneous velocity, but unless you
intend to analyze detailed dynamical properties of the system, you
don't really need it: just use the temperature command to generate
adequately-distributed random velocities.

You can recover the cell dimensions from the DCD trajectory using VMD.
Load the PSF and DCD files, display the last frame, and use (in the
console) the following command:
pbc get -namd

Jerome

2010/1/27 Raul Araya <arayasecchi_at_gmail.com>:
> 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?
>
> 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;
> http://www.cbuc.cl
>
>

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