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?



This archive was generated by hypermail 2.1.6 : Tue Dec 31 2013 - 23:21:37 CST