Re: How to solve the out of cell box for long time in Periodic Boundary Conditions?

From: Jérôme Hénin (
Date: Thu May 20 2010 - 10:00:08 CDT

You can fix that with VMD and the pbctools plugin. See e.g. this thread:

as well as the documentation:


On 20 May 2010 04:06, Aurum Bai <> wrote:

> Hello, everyone.
> I use namd to simulate the protein and ligand for long time. Then I found
> the ligand vanish at the boundary of cell box, while appear another
> boundary, but the protein not. The problem is normal, because I use the
> "Periodic Boundary Conditions".
> But It brings some problem to calculate the rmsd and binding energy and so
> on, because the coordnates of ligand had been changed.
> How do I deal with this problem, and calculate the rmsd correctly?
> Thanks
> javacfish

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