Unit cell information in binary output files

From: Ben Roberts (Benjamin.P.Roberts_at_vcp.monash.edu.au)
Date: Tue Sep 05 2006 - 22:23:13 CDT

Hi List,

I am trying to run a long (multi-nanosecond) simulation in NAMD at a
supercomputer centre. Because of the CPU usage policies at this centre,
I can't run the entire simulation at once: it must be split up into a
series of smaller simulations.

This is a constant-pressure simulation, so the unit cell size changes
slightly during the course of the simulation. I'm aware that the unit
cell size needs to be accurate for the start of each simulation: too
small and the simulation blows up, too large and gaps of empty space
arise. (Especially, I'm keen to avoid the "cell too small" problem).

Now, the only way I know of to activate periodic boundary conditions and
set the unit cell size in a simulation (even one that serves to continue
on from the finish of another simulation) is to set the parameters
cellBasisVector1, cellBasisVector2, cellBasisVector3, and cellOrigin.

It would make life easier for me if the unit cell size is somehow
present in the simulation input, that is, the .coor and/or .vel files
(which I am currently outputting in binary format for greater accuracy).
Is the unit cell size stored in these files at all, and if so, how would
I go about accessing it? For example, is there a parameter in the input
file I can turn on that translates as "Read unit cell data from .coor file"?

Alternatively, if this information is not written to .coor or .vel
files, is it written to restart files?

I know about the .xsc file (and its counterpart the .xst file), and am
aware that it's possible to read the unit cell data from there and
manually overwrite whatever previously existed in the input file, and
that this can in principle be automated by a script. I also know that
unit cell information is optionally present in the .dcd file, but that
extracting it from there would be at least as tricky as pulling it out
of the .xsc file.

Any help appreciated.



Benjamin P. Roberts, B.Sc.(Hons)
Ph.D. Student
Department of Medicinal Chemistry
Victorian College of Pharmacy (Monash University)
381 Royal Parade, Parkville VIC 3052, Australia
Phone +61 3 9903 9561 | Fax +61 3 9903 9582 | Mobile +61 401 784 940

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