Re: ABF simulations

From: Chris Chipot (
Date: Tue Jul 29 2008 - 09:55:41 CDT

Dear Raúl,

if you are familiar with the NAMD implementation of ABF, the order
parameter used for this work is "zcoord", i.e. the distance between
the center of mass of glycerol to that of the channel, projected
onto the z-direction of Cartesian space.

As indicated in the paper, the reaction pathway was broken into
several adjacent windows. The initial configurations for these
different windows came from an initial steered-molecular dynamics
work by the Schulten group. Note that you can generate the initial
configurations by covering the reaction pathway sequentially and
equilibrating the new starting point carefully.

Given the slow relaxation of the different degrees of freedom, in
particular at the level of the selectivity filter, the choice of
the threshold number of force samples accrued prior to applying the
biasing force is crucial. We tried up to 5,000 samples to get a
reasonable estimator of the average force. Too small a threshold
is prone to yield non-equilibrium effects which ought to be avoided.

Chris Chipot

Raul Araya a écrit :
> Dear NAMD users: (Specially those related to ABF simulations)
> I have been reading the paper from the Shulten group (Henin,
> Tajkhorshid, Shulten, Chipot. Biophysical Journal Vol. 94, February 2008
> 832-839) and Im interested in performing this kind of methodology to
> pass a solute trough a membrane channel. The paper is clear about the
> ABF method used, and also is the ABF turotial for NAMD, but nevertheless
> I will like to get more details about how the methodology was
> implemented for this GlpF + Glicerol ABF simulation. Im interested
> mostly in how the initial configuration for each window was established,
> what type of coordinate was chosen, and in general a little more detail
> about the ABF simulation in this particular case.
> thanks
> -- Raúl Araya Secchi
> B.Sc Molecular Biotechnology.
> Molecular Biotechnology Engineer.
> Centre for Bioinformatics CBUC,
> Faculty of Biological Sciences, P. Universidad Catolica de Chile
> Portugal # 49 – ZIP 6513492 Santiago – Chile Phone: + 56 2 6862269;

Chris Chipot, Ph.D.
Equipe de dynamique des assemblages membranaires
Unité mixte de recherche CNRS/UHP No 7565
Université Henri Poincaré - Nancy 1           Phone: (33) 3-83-68-40-97
B.P. 239                                      Fax:   (33) 3-83-68-43-87
54506 Vandoeuvre-lès-Nancy Cedex
              The wretch, concentred all in self,
              Living, shall forfeit fair renown,
              And, doubly dying, shall go down
              To the vile dust, from whence he sprung,
              Unwept, unhonored, and unsung.            Sir Walter Scott

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