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

From: J閞鬽e H閚in (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Thu May 20 2010 - 10:00:08 CDT

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Hi,
You can fix that with VMD and the pbctools plugin. See e.g. this thread:
https://www-s.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/15027.html

as well as the documentation:
http://www.ks.uiuc.edu/Research/vmd/plugins/pbctools/

Cheers,
Jerome

On 20 May 2010 04:06, Aurum Bai <javacfish_at_yahoo.com.cn> 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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