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

[OZGE ENGIN]

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.