Re: question about cellBasisVector*?

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Tue Jan 13 2009 - 09:33:20 CST

Hi Bin,

>From the description of extendedSystem in the manual
(http://www.ks.uiuc.edu/Research/namd/2.6/ug/node31.html):
 In addition to .coor and .vel output files, NAMD generates a .xsc
(eXtended System Configuration) file which contains the periodic cell
parameters and extended system variables, such as the strain rate in
constant pressure simulations. *Periodic cell parameters will be read
from this file if this option is present, ignoring the above
parameters*. (emphasis mine)

If pressure control is on, namd will use extendedSystem or
cellBasisVector for the *initial* cell size, but it will be changed
during the simulation.

Best,
Peter

BIN ZHANG wrote:
> Hi, all:
>
> I have a question about cellBasisVector:
>
> If cellBasisVector* and extendedSystem are both given, and they are not
> exactly the same, then which one will be used by NAMD for Periodic
> Boundary Condition?
> Also, if langevinPiston is on, which leads to the change of cell size,
> then will NAMD still use cellBasisVector for PBC or it will change it
> internally?
>
> Thanks a lot.
>
> Bin
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> -------------------------------------------------------------
> The tree of liberty must be refreshed from time to time with the blood
> of patriots and tyrants.

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