From: Chris Chipot (Christophe.Chipot_at_edam.uhp-nancy.fr)
Date: Sun Nov 05 2006 - 03:26:53 CST
Ugur,
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
E-mail: Christophe.Chipot_at_edam.uhp-nancy.fr
http://www.edam.uhp-nancy.fr
To sin by silence when we should protest makes cowards out of men
Ella Wheeler Wilcox
_______________________________________________________________________
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