[gmx-users] periodic boundary conditions
David van der Spoel
spoel at xray.bmc.uu.se
Tue Mar 23 08:51:01 CET 2004
On Mon, 2004-03-22 at 23:30, Marc Vogt wrote:
> I'm trying to run simulations with periodic boundary conditions and recently
> found the follwing lines in my .log file
> Removing pbc first time
> Done rmpbc
> I have pbc = xyz in the mdp file
this is just fine. The messages are just to indicate that the PBC was
done succesfully the first step. They are also done at all other time
> are the periodic conditions being turned off?
> do I need to set set GMXFULLPBC equal to 1? What is the purpose of this
> environment variable? I can't find it in the manual (3.2) appendix.
> Is it no longer an environment variable in 3.2?
This environment var is replaced by
pbc = full
but it is only necessary for special cases. It is somewhat slower than
pbc = xyz, therefore it is optional.
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David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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