VMD-L Mailing List
From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Apr 09 2014 - 11:35:28 CDT
So far as I know, the "CORD" string is all that ever gets written
to a DCD header, but I would be curious to learn otherwise...
On Mon, Apr 07, 2014 at 08:56:05AM +0200, Norman Geist wrote:
> > -----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.
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-- NIH Center for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801 http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349 http://www.ks.uiuc.edu/Research/vmd/