Re: CoM motion not removed

From: Jim Phillips (
Date: Mon Feb 23 2004 - 11:01:02 CST


This is normal. If you fix or restrain any part of the molecule, the
remaining atoms will oscillate relative to the fixed part. Since the
system is restrained, the time-averaged momentum will be zero.


On Wed, 18 Feb 2004, Neema Salimi wrote:

> When doing a simulation with a protein fixed and surrounded by solvent, I have
> noticed that CoM motion is not removed at the beginning of the simulation.
> However, in the same system, when the protein is not fixed, the CoM motion is
> removed. In addition, the values of the momenta written out by NAMD are much
> larger for the fixed protein system than the unfixed protein system. How
> can I fix
> this?
> Neema Salimi
> Graduate Student - Agard Laboratory
> Program in Biophysics
> University of California, San Francisco

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