ABF calculations

From: jia (jia_at_ornl.gov)
Date: Mon Nov 19 2007 - 14:33:51 CST

Dear NAMD users and Jerome,

I'm trying to use ABF method to calculate the binding energy of two small size
proteins, 140 a.a for one and 57 for another, and I'm wondering if it's a good
idea to choose the reaction coordinate as the distance separating the centers
of mass of these two domains given the fact that many atoms will be
participating to the center of mass. Any suggestions will be appreciated.
Thanks much!


Postdoc Research fellow
Center for Molecular Biophysics,
Oak Ridge National Lab
Oak Ridge, TN, 37830

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