<div> </div>
<div>Regarding the peptide moving out of the box, it is only a visualization artifact.</div>
<div>Try trjconv -pbc inbox.<br><br> </div>
<div><span class="gmail_quote">2007/11/5, OZGE ENGIN <<a href="mailto:OZENGIN@ku.edu.tr">OZENGIN@ku.edu.tr</a>>:</span>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Hi all,<br><br>I am performing a simulation of peptide at air/water interface.<br><br>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.
<br><br>Although I expanded the box only in the z direction, what may be the probable reason for this?<br><br>Ozge.<br><br>_______________________________________________<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">
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