VMD-L Mailing List

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Mon Apr 07 2014 - 01:56:05 CDT

> -----Ursprüngliche Nachricht-----
> Von: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] Im
> Auftrag von Axel Kohlmeyer
> Gesendet: Freitag, 4. April 2014 13:37
> An: Marcela Madrid
> Cc: Vmd l
> Betreff: Re: vmd-l: writing velocities from VMD
>
> hi marcela,
>
> only very few file format plugins for VMD support reading velocities
> and even less support writing (as far as i can tell the HOOMD plugin
> and the TNG plugin). for the rest you would have to copy the
> velocities to coordinates and save them as coordinates.
>
> the molfile API has no facility at this moment to write two files in
> parallel, as it would be required in the case of a DCD file, so the
> only option to extract the velocities would be to copy them to
> coordinates (if needed in a new "molecule") via Tcl script and then
> write them out as coordinates. of course that has the downside that
> you now have the "CORD" magic string in the header that identifies the

Which shouldn't be a problem, as NAMD itself writes its veldcds with that
same magic string. Otherwise most DCD readers wouldn't recognize the file to
be DCD. I though this is a forced property of a DCD file, is there a special
magic string for velocities known, just for my interest?

> file as a file containing coordinates.
>
> axel.
>
> On Thu, Apr 3, 2014 at 8:31 PM, Marcela Madrid <mmadrid_at_psc.edu> wrote:
> > hi
> >
> > How do I write velocities into a dcd file (or any other format) with
> VMD?
> > I am loading a trajectory in Desmond format, and I do not see the
> option
> > to write velDCD, I only seem successful in writing coordinates.
> > Thanks so much!
> > Marcela
> >
> >
> >
> >
> >
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> College of Science & Technology, Temple University, Philadelphia PA,
> USA
> International Centre for Theoretical Physics, Trieste. Italy. 

---
Diese E-Mail ist frei von Viren und Malware, denn der avast! Antivirus Schutz ist aktiv.
http://www.avast.com