Re: Unit cell information in binary output files

From: Marcos Sotomayor (
Date: Tue Sep 05 2006 - 23:41:42 CDT

Hi Ben,

What about using the command extendedSystem?

you can read the unit cell information by typing

extendedSystem mysimulation.restart.xsc

in the NAMD configuration file.


On Wed, 6 Sep 2006, Ben Roberts wrote:

> 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.
> Thanks,
> Ben
> --
> 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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