Re: molecule jumps from one site to the other?

From: Eric H. Lee (ericlee_at_ks.uiuc.edu)
Date: Mon Jul 13 2009 - 21:33:42 CDT

There is nothing wrong your trajectory. What you are observing is NAMD
wrapping the coordinates to whichever periodic box the molecule is
mostly in. You can use PBCTools to unwrap your trajectory, or just turn
off "wrapall" in your configuration script when running the simulation.

-Eric Lee
Theoretical and Computational Biophysics Group, UIUC

uu zhu wrote:
> 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
> molecule always 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?
> Thanks.
> Best regards,
> --
> WANG
> PhD
> Division of Bioengineering
> School of Chemical & Biomedical Engineering
> Nanyang Technological University
> Singapore

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