Re: ABF on a single molecule

From: Ugur Akgun (
Date: Mon Nov 06 2006 - 14:19:04 CST

Thank you Chris. What about these 3 variables?


>From: Chris Chipot <>
>To: Ugur Akgun <>
>Subject: Re: namd-l: ABF on a single molecule
>Date: Sun, 05 Nov 2006 10:26:53 +0100
>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:
> To sin by silence when we should protest makes cowards out of men
> Ella Wheeler Wilcox

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