VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu Jul 14 2011 - 09:23:45 CDT

On Thu, Jul 14, 2011 at 6:18 AM, Nima Nouri <nouri.f.nima_at_gmail.com> wrote:
> Hi everybody
>
> I am wondering if someone could give me a help on how to add user outputs
> (eg. virial) to a DCD trajectory file, specially for VMD.
> Even I would be glad to know even it is possible or not?

no, it is not. the dcd format is for coordinates (or velocities or forces) only.

> If yes please give me a clue on how to.

> If no please show me a powerful alternative file output.

the only format that i know that is flexible enough would
be the lammps custom (text mode) dump format. however,
that still won't get you direct access to the data in a user
field, since the molfile plugin API doesn't support that.
for lammps custom dumps, i have implemented a workaround:
http://sites.google.com/site/akohlmey/software/lammps-icms#TOC-Notes
but it is messy and won't help you for a property where you
need to communicate 6 items (or you have to give up coordinates,
or you cannot have the property change).

axel.

>
> --
> Best Regards
> N.Nouri
>
> Ph.D Student
> Department of Mechanical Engineering
> Isfahan University of Technology
> Isfahan, Iran
> 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.