Re: Steered Molecular Dynamics for more than one atom

From: David Tanner (
Date: Mon Aug 10 2009 - 15:31:09 CDT

The center-of-mass doesn't put a velocity on the atoms, it puts a
force on the other atoms. Each atom being pushed is connected to the
center-of-mass by a spring. Each atom then gets dragged along by those

David E. Tanner
Theoretical and Computational Biophysics Group
3159 Beckman Institute
University of Illinois at Urbana-Champaign
405 N. Mathews
Urbana, IL 61801

On Aug 10, 2009, at 1:55 PM, gaurav bhatti wrote:

I am currently running a steered molecular dynamics in which I am
trying pull as many as 2300 atoms in one domain away from another
domaimn with a very small velocity of 1 Angstrom per ns . I went
through the tutorial for smd available on the namd website which
mentions that when moving multiple atoms, the dummy atom is attached
to the center of mass and then pulled with the specified velocity.
However from the tutorial it is not clear how the velocity applied to
the center of mass is transferred to the individual atoms? Is it the
same for all atoms or depends their position relative to the center of
mass? Also how about the direction of motion for the individual atoms?

Gaurav Bhatti
Wayne State University

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