[gmx-users] unexpecter rmsd

[Justin Lemkul]

On 3/27/20 11:10 AM, Emran Heshmati wrote:
> Thanks to Paul and jorden, I repost my question:
> I am working on a protein consisting 2 chains. After performing
> regular MD simulation
> and analysis the outputs, I got unexpecter rmsd, as seen in link below.
> What is the problem??
> https://www.4shared.com/photo/cYHAiZgJea/New_Doc_2020-03-27_042856.html

This is a PBC effect, with one or more protein chains jumping across a 
periodic boundary. Recenter with trjconv. You may have to center on one 
of the chains individually to get proper wrapping of the unit cell.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================