[gmx-users] RE: Molecule out of pbc box

Mark Abraham mark.abraham at anu.edu.au
Thu Aug 26 16:21:19 CEST 2010

----- Original Message -----
From: Nimesh Jain <nimeshjain2010 at u.northwestern.edu>
Date: Friday, August 27, 2010 0:15
Subject: [gmx-users] RE: Molecule out of pbc box
To: Discussion list for GROMACS users <gmx-users at gromacs.org>

> Hi,
> Does anyone know if there is a way to put a molecule back in the pbc box in gromacs. I am visualizing my sims in vmd and the molecule keeps going out of the box. Is it normal or an artifact in vmd, is there a way to put the molecule back in the box? please let me know.

Yes. See http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

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