RE: write out the snapshot from MD trajectory

From: mjyang (
Date: Fri Aug 27 2010 - 10:28:25 CDT

Dear Eddi,
   I read through the PBCtools manuals and tested the commands, but I still can't construct a fully solvated protein from the MD snapshot in which the protein has protruded the unit cell.
   Could you please give more details of how to do the job?

Thanks in advance.


From: Eduard Schreiner []
Sent: Friday, August 27, 2010 6:55 PM
To: mjyang
Subject: Re: namd-l: write out the snapshot from MD trajectory

check the pbctools plugin


On Fri, Aug 27, 2010 at 4:59 AM, mjyang <> wrote:
> Dear NAMD users,
> I performed a NPT MD simulation by NAMD under periodic condition for 40
> ns. But the protein protrudes out of the water box along MD trajectory.
> Could someone please tell me how to write out the snapshot at 40ns with the
> protein located at the center of the box?
> Many thanks.
> Mingjun

Eduard Schreiner
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
Phone: 217-244-4361
Fax: 217-244-6078

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