Re: Steered Molecular Dynamics

From: Chris Harrison (
Date: Wed Aug 05 2009 - 08:46:52 CDT

What you are actually asking is not clear. Precise and clearly written
questions receive the most assistance.

If you're asking can you use the centers-of-mass as your "anchor" and
"pulling point": yes, but it's up to you as the scientist to determine if
it's a reasonable approximation for use in modeling your system's "real"

If your question is: how do I define direction of pulling? I suggest
strongly working through the NAMD tutorial in which you learn how to perform
SMD and set the direction/vector of pulling.

Required files:


Chris Harrison, Ph.D.
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                            Voice: 217-244-1733               Fax: 217-244-6078
On Fri, Jul 31, 2009 at 12:33 AM, gaurav bhatti <>wrote:
> Hi
> I posted my question in some other thread earlies. I am sorry for the
> mistake.
> I want to use steered molecular dynamics to pull two domains of a protein
> apart from each other. I plan to do in by constraining domain 1 and applying
> a constant velocity to the domain 2. I know that I can constrain domain 1 by
> setting the B or Occupancy column of these atoms as 1 and using that as
> reference for constraints. Also I think I can select the SMD atoms in the
> same way. My problem is with the direction of pulling. I can calculate the
> center of masses of the two domains and then apply velocity along the
> direction : COM2 - COM1. Is this  a good strategy?
> Gaurav Bhatti
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