Re: NAMD trajectory format

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Wed May 28 2008 - 09:05:46 CDT

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
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If you make something idiot-proof, the universe creates a better idiot.

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