From: mjyang (mjyang_at_hku.hk)
Date: Fri Aug 27 2010 - 10:28:25 CDT
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 [eduard.schreiner_at_gmail.com]
Sent: Friday, August 27, 2010 6:55 PM
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 <mjyang_at_hku.hk> 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.
-- -- ============================================================================= 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 http://www.ks.uiuc.edu/~eschrein/ =============================================================================
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:54:27 CST