Re: NAMD trajectory format

From: Konrad Hinsen (hinsen_at_cnrs-orleans.fr)
Date: Wed May 28 2008 - 07:35:17 CDT

On 27.05.2008, at 12:27, Axel Kohlmeyer wrote:

> the best way to read NAMD trajectories (and many other formats) is
> through molfile plugin interface from VMD. the .dcd format is taken
> from x-plor/charmm and as such not exactly thoroughly documented.

That's an interesting idea but it doesn't look simple. I'd have to
implement a plugin loading and handling system compatible with VMD's.

On the other hand, taking VMD's plugins as an inspiration does sounds
like a very good idea. Unfortunately it seems that the current source
code distributions don't contain the plugins any more. Where did you
find dcdplugin.c? Do I have to request CVS access to get it?

> please see the molfile code. for your convenience here is the unitcell
> decoding section of the dcdplugin.c file:

Thanks, that was very useful! I assume that the conventions for
reconstructing the three lattice vectors are the same as in
crystallography: a along the x-axis, b in the x-y-plane.

> i don't know for sure, but i would suspect it serves as a
> reference point for PBC wrapping. in any case it should be
> irrelevant for analysis of trajectory data that was written
> with recent NAMD versions (2.6 and onward) where you have
> all required information in the .dcd file.

That would be nice of course... but I still wonder why any
unnecessary information would be written out to a file at each time
step.

Thanks for your help,
   Konrad.

--
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Konrad Hinsen
Centre de Biophysique Moléculaire, CNRS Orléans
Synchrotron Soleil - Division Expériences
Saint Aubin - BP 48
91192 Gif sur Yvette Cedex, France
Tel. +33-1 69 35 97 15
E-Mail: hinsen_at_cnrs-orleans.fr
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