RE: How to calculate free energy for conformational change

From: gaurav bhatti (
Date: Thu Jul 30 2009 - 23:51:05 CDT


I want to use steered molecular dynamics to pull two domains of a
protein apart from each other. I plan to do in by constraining domain 1
and applying a constant velocity to the domain 2. I know that I can
constrain domain 1 by setting the B or Occupancy column of these atoms
as 1 and using that as reference for constraints. Also I think I can
select the SMD atoms in the same way. My problem is with the direction
of pulling. I can calculate the center of masses of the two domains and
then apply velocity along the direction : COM2 - COM1. Is this a good

Gaurav Bhatti

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