Re: NAMD trajectory format

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed May 28 2008 - 11:18:26 CDT

Hi,
  Just FYI, the source distribution tar files _do_ include the plugin
sources -- they are in a top level "plugins" directory, not inside the
"vmd" source directory. CVS is of course the most up-to-date source base.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, May 28, 2008 at 10:05:46AM -0400, Axel Kohlmeyer wrote:
> On Wed, 28 May 2008, Konrad Hinsen wrote:
>
> KH> On 27.05.2008, at 12:27, Axel Kohlmeyer wrote:
> KH>
> KH> >the best way to read NAMD trajectories (and many other formats) is
> KH> >through molfile plugin interface from VMD. the .dcd format is taken
> KH> >from x-plor/charmm and as such not exactly thoroughly documented.
> KH>
> KH> That's an interesting idea but it doesn't look simple. I'd have to implement
> KH> a plugin loading and handling system compatible with VMD's.
>
> it is not that difficult and you could use the fortran wrapper code
> that i contributed as a starting point. OTOH, you can also just link
> the individual subroutines as a static library. see:
>
> http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/
>
> and particularly:
>
> http://www.ks.uiuc.edu/Research/vmd/plugins/doxygen/callmolfileplugins.html#callmolfileplugins
>
> KH> On the other hand, taking VMD's plugins as an inspiration does sounds like a
> KH> very good idea. Unfortunately it seems that the current source code
> KH> distributions don't contain the plugins any more. Where did you find
> KH> dcdplugin.c? Do I have to request CVS access to get it?
>
> hmmm... you are right and they are not in the plugin update distribution
> either. looks like it might be a good idea to have a molfile plugin
> source tarball available somehwere.
>
> yes, i have cvs access (not hard to get), since i occasionally
> contribute a line or two of code. ;)
>
> KH> >please see the molfile code. for your convenience here is the unitcell
> KH> >decoding section of the dcdplugin.c file:
> KH>
> KH> Thanks, that was very useful! I assume that the conventions for
> KH> reconstructing the three lattice vectors are the same as in crystallography:
> KH> a along the x-axis, b in the x-y-plane.
>
> correct.
>
> KH> >i don't know for sure, but i would suspect it serves as a
> KH> >reference point for PBC wrapping. in any case it should be
> KH> >irrelevant for analysis of trajectory data that was written
> KH> >with recent NAMD versions (2.6 and onward) where you have
> KH> >all required information in the .dcd file.
> KH>
> KH> That would be nice of course... but I still wonder why any unnecessary
> KH> information would be written out to a file at each time step.
>
> restarting?
>
> cheers,
> axel.
>
> KH>
> KH> Thanks for your help,
> KH> Konrad.
> KH> --
> KH> ---------------------------------------------------------------------
> KH> Konrad Hinsen
> KH> Centre de Biophysique Moléculaire, CNRS Orléans
> KH> Synchrotron Soleil - Division Expériences
> KH> Saint Aubin - BP 48
> KH> 91192 Gif sur Yvette Cedex, France
> KH> Tel. +33-1 69 35 97 15
> KH> E-Mail: hinsen_at_cnrs-orleans.fr
> KH> ---------------------------------------------------------------------
> KH>
> KH>
> KH>
>
> --
> =======================================================================
> Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://www.cmm.upenn.edu
> Center for Molecular Modeling -- University of Pennsylvania
> Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
> tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
> =======================================================================
> If you make something idiot-proof, the universe creates a better idiot.

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078

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