RE: Question about equilibration

From: Reichert, David (
Date: Wed Jun 15 2011 - 14:21:33 CDT

One thing you might consider is gradually removing the constraints so that they aren't suddenly turned off.
David E. Reichert, PhD.
Assoc. Professor of Radiology
Washington University School of Medicine

voice: 314-362-8461
fax: 314-362-9940

From: [] On Behalf Of snoze pa
Sent: Wednesday, June 15, 2011 11:20 AM
Subject: Re: namd-l: Question about equilibration

Please find the link to check the deformed protein
On Wed, Jun 15, 2011 at 11:07 AM, snoze pa <<><>> wrote:
Dear NAMD Users,

I need some explanation regarding my protein equilibration. I see my protein gets deformed during the equilibration. Do you think it is okey?
To add one more note about the protein deformation. First I used harmonic constrained during the equilibration. Then the restrain were removed and protein was again equilibrated. I am getting deformation after removing harmonic constraints. In this step during first 600 ps it is fine but last 300 ps the protein is getting deformed.

I will highly appreciate your help.

Thank you


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