molecule jumps from one site to the other?

From: uu zhu (
Date: Mon Jul 13 2009 - 21:11:52 CDT

Hi all,
Recently, I checked one of NPT 's DCD files, and found that in VMD one
molecule "suddenly" jumps from site A to site B, and jumps back again. This
action happens several times during DCD trajectory. Since the
moleculealways jumps, the trajectory is hard to do analysis. I thought
it could come
from the periodic boundary condition. Does anyone know how to set the
parameters to forbid such jumping? Or could we set some parameters to get
the "real" and normal trajectory in VMD?
Best regards,

Division of Bioengineering
School of Chemical & Biomedical Engineering
Nanyang Technological University

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