[gmx-users] strange movement

David spoel at xray.bmc.uu.se
Wed Jan 14 20:07:00 CET 2004

On Wed, 2004-01-14 at 19:56, Xavier Periole wrote:
> I could be just the consequence of the exit of the first residue of the 
> two subunits
> of the box limits, which results in a strange reconstruction of your system.
> I guess that playing with the -pbc option will fix this problem.
> You migh consider constrain the CM of your pentamer at the center of
> the box.
Use trjconv -pbc cluster or trjconv -pbc inbox or something like that
> XAvier
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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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