Re: Translocation problem while attempting to use ABF

From: Hugh Martin (hughtendo_at_gmail.com)
Date: Wed Aug 05 2009 - 12:26:30 CDT

Hi again,

When I ran the simulation with a reduced force constant, the moving atom
proceeded to translocate to the centre of xiMin and xiMax at a much slower
rate, so it is indeed this parameter which is causing this. I find this
confusing, as my understanding is that the force constant should only be
active at the walls of xiMin and xiMax and not inbetween (according to the
user guide and tutorial). So is it the NAMD2.6 PBC implementation that is
causing the force constant to be applied where it shouldn't? I attempted to
use NAMD2.7b1 and found that a similar phenomenon was occuring.

Also, having read the following papers:

*Calculating free energies using average
force*<http://dx.doi.org/10.1063/1.1410978>,
Eric Darve and Andrew Pohorille
*Overcoming free energy barriers using unconstrained molecular dynamics
simulations* <http://dx.doi.org/10.1063/1.1773132>, Jérôme Hénin and
Christophe Chipot

 *Exploring the free-energy landscape of a short peptide using an average
force* <http://dx.doi.org/10.1063/1.2138694>, Christophe Chipot and Jérôme
Hénin
I feel that I have a solid understanding of the theory behind ABF, however,
I'm unsure of a couple of points: When the ABF force is applied, the moving
atom is "allowed" to make its way to the next reaction coordinate bin via
diffusion, at this point the net force acting on the atom is roughly zero
when considering both the free energy landscape and the applied ABF force..--001636c5a850efbd110470684eae--

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