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

From: Davide Branduardi (
Date: Thu Feb 02 2012 - 14:27:18 CST

Hi Paulo,

        I do not know specifically about the features already present in NAMD but I guess you can do it pretty
easily by using PLUMED. There you can specify a set of atoms for the alignment and a set for a measure, as
you might need for protein ligand interaction. The only drawback is that there you do not have ABF there (but metadynamics
for example) so, in case you need ABF better to wait for next NAMD release, as recommended by Giacomo.


On Feb 2, 2012, at 7:19 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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