Regarding the peptide moving out of the box, it is only a visualization artifact. Try trjconv -pbc inbox.
2007/11/5, OZGE ENGIN <[EMAIL PROTECTED]>: > > 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. > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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