[gmx-users] pbc in xy only

David van der Spoel spoel at xray.bmc.uu.se
Tue Mar 13 07:21:42 CET 2007

Wael Soliman wrote:
> Hello Every one,
> I want to do a simulation with periodic images just in X and Y planes 
> but not in Z direction, but when I write pbc = xy in the mdp fine it 
> always gives me error saying chosse either xyz or no,
> os is it possible to do periodic conditions in just two planes? and if 
> so how to do it? I will appreciate if any body could help me in this 
> problem,
> thanks for your concern
easiest way is to extend the box on Z direction by a factor of three, 
use pbc=xyz and the right pme geometry.

David van der Spoel, PhD, Assoc. 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://folding.bmc.uu.se

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