Re: ABF on a single molecule

From: Chris Chipot (
Date: Sun Nov 05 2006 - 03:26:53 CST


writing of comprehensive ABF tutorial is currently underway. What I
can tell you from now is that according to your message, if you want
to define as a reaction coordinate the projection onto the z-axis of
the vector that connects the COM of your molecule to that of your
channel - the latter COM being evaluated from a subset of atoms -
you ought to use:

abf coordinate zCoord
abf abf1 {indices of atoms forming the COM of the
                          channel (no comas needed)}
abf abf2 {indices of atoms forming the COM of the
                          molecule diffusing in the channel}

Chris Chipot

Ugur Akgun wrote:

> I am using ABF for the first time, I am trying to move a single molecule
> through the z-axis of a channel to get the free energy profile. I could
> not figure out how to create the conf file.
> Is there any example you can share?
> thank you


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 Vandœuvre-lès-Nancy Cedex, France


       To sin by silence when we should protest makes cowards out of men
                                                     Ella Wheeler Wilcox

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