RE: rmsd is not stabilizing even after 0.6 ns

From: Ana Celia Araujo Vila Verde (
Date: Tue Oct 31 2006 - 14:27:23 CST

How big is the RMSD? If it is not bigger than 3-6 A, I think it is reasonable to run for longer (say 3 ns). Check your structure and see what it is doing, in any case.


From: on behalf of Dhiraj Srivastava
Sent: Tue 10/31/2006 2:41 PM
Subject: namd-l: rmsd is not stabilizing even after 0.6 ns

Hi all
        I am trying to equilibrate my system in NPT ensemble but even after 0.6 ns of equilibration rmsd is not getting stabilized and keeps on increasing. is there any problem in my system or should i try to equilibrate for some more time.

Dhiraj Kumar Srivastava
Department of Chemistry
University of Missouri-Columbia
MO, 65211
Ph. no. 001-573-639-0153 

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