Steered Molecular Dynamics for more than one atom

From: gaurav bhatti (
Date: Mon Aug 10 2009 - 13:55:10 CDT

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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