From: Roman Petrenko (rpetrenko_at_gmail.com)
Date: Tue Nov 17 2009 - 22:51:27 CST
NAMD doesn't ! You indicate it in the config file.
cellBasisVector1 Ax Ay Az
..
..
cellOrigin
or if you use restart, it is written in the *.xsc files produced by
NAMD after the first run.
On Tue, Nov 17, 2009 at 11:16 PM, Michael Thomas
<exploding.dinosaurs_at_gmail.com> wrote:
> Hi everyone,
>
> How does NAMD calculate the size of the periodic box during the simulation?
> Where exactly do the numbers for the box's vectors in the xst file come
> from?
>
> Thanks,
>
> Michael
>
>
-- Roman Petrenko Physics Department University of Cincinnati
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