Question about ABF

From: Gaurav Sharma (sharma_at_coe.neu.edu)
Date: Wed Oct 25 2006 - 18:03:13 CDT

Hi All,

I am using the ABF method to study the free energy change when two
chains of my protein move apart during the MD run (this conformational
change is induced by electrostatic repulsions between the chains). For
this I used the distance-com RC method by defining a set of atoms on
each chain as abf1 and abf2. I was not sure if I should use the external
bias force since the two chains move apart by themselves so I performed
two simulations one with applyBias on and one with it turned off
expecting to get the same result in both cases. But the two results are
markedly different as can be seen from the attached file.

I need some insight as to how to interpret the results to find out which
is a more appropriate method. I also read the original Henin & Chipot
paper on 'Overcoming free energy barriers....' The results for
deca-alanine (Fig 1) gives free energy profiles for unconstrained and
constrained simulations. Maybe I missed it but what are the constraints
in the simulation?

Thanks in advance for your help.

Gaurav

-- 
Gaurav Sharma
Computational BioNano Robotics Lab
Northeastern University
Boston, MA - 02115
Tel: 617-373-2970
http://www.bionano.neu.edu/ 

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