NAMD trajectory format

From: Konrad Hinsen (hinsen_at_cnrs-orleans.fr)
Date: Tue May 27 2008 - 02:41:29 CDT

Dear NAMD users,

I am trying to figure out the exact meaning of the information
contained in a trajectory (dcd + xst) produced by NAMD, for use in an
analysis program. Ideally, I would like my program to handle any NAMD-
produced trajectory correctly. I looked at the manual, of course, but
this was not sufficient.

What is not clear to me is the interpretation of constant-pressure
trajectories. There is information about the size and shape of the
box in the dcd file, but also in the xst file. The dcd file has six
numbers per step for which I have no documentation. The example file
I received from a colleague is rectangular, so it is not sufficient
to completely decode the six numbers.

The xst file has three vectors per time step, which is clear enough.
However, is it safe to assume that
1) there is an xst file for every constant-pressure trajectory?
2) the box size/shape information is available for the same time
steps that are recorded in the dcd file?

The other unclear point concerns the "cell origin" data. After
reading the manual, it is not clear to me how exactly this data
enters in the interpretation of the coordinate sequences. In my
example file, the cell origin is constant over the trajectory, but I
suppose this is not always the case (otherwise there would be no need
to record it at every time step). What exactly is this cell origin?
The fixed central point of the coordinate scaling? An offset to be
added to the coordinates? Or yet something else?

Thanks in advance for any 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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