Re: RMSD collective variable - Different atons to align and to calculate RMSD

From: Giacomo Fiorin (
Date: Thu Feb 02 2012 - 13:52:49 CST

At the moment, they should be the same. Different groups for alignment and
RMSD calculation will be in the next release.


On Thu, Feb 2, 2012 at 1:19 PM, Paulo Cesar Telles de Souza <> wrote:

> Dear colleagues
> I'm trying to use the ABF method to get the free energy difference
> between two conformation states of a protein. For this, I tried to use
> as a reaction coordinate the RMSD of these two conformations, so that
> I get a 2D graph (RMSD conformation 1 x RMSD conformation 2, with the
> free energy differences given by a color scale). However I have a
> question regarding the use of RMSD as a collective variable in the
> NAMD program: Can I specify, in the RMSD collective variable,
> different atoms for the alignment of protein and to calculate the RMSD
> itself. Or must they necessarily be the same in the NAM program?
> Thanks
> Paulo

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