[gmx-users] Performing simulation at air/water interface

Pedro Alexandre de Araújo Gomes Lapido Loureiro palaplou at gmail.com
Mon Nov 5 19:33:26 CET 2007

Regarding the peptide moving out of the box, it is only a visualization
Try trjconv -pbc inbox.

2007/11/5, OZGE ENGIN <OZENGIN at ku.edu.tr>:
> Hi all,
> I am performing a simulation of peptide at air/water interface.
> The box vectors are: x,y,z where 2x=2y=z. After loading the trajectory to
> the vmd, I realized that water molecules moved out of bulk water in the z
> direction: into the vacuum. However, the peptide also moved out of the bulk
> water, but at this time, not in the z direction but in the x direction.
> Although I expanded the box only in the z direction, what may be the
> probable reason for this?
> Ozge.
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