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

From: Paulo Cesar Telles de Souza (paulocts_at_gmail.com)
Date: Thu Feb 02 2012 - 12:19:10 CST

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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