Re: Steered Molecular Dynamics for more than one atom

From: Marcos Sotomayor (
Date: Mon Aug 10 2009 - 21:11:11 CDT

Just consider the actual potential applied to the system:

U(\vec{r1},\vec{r2},....,t)=1/2k[vt-(\vec{R(t)}-\vec{R(0)})dot \vec{n}]^2

where R(t) should be replaced for an expression for the center-of-mass

Take -grad_ri and you will get the force on the corresponding atom i.


On Tue, 11 Aug 2009, 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
> _________________________________________________________________
> We all see it as it is. But on MSN India, the difference lies in perspective.

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:53:09 CST