Re: ABF on a single molecule

From: Ugur Akgun (ugur_iowa_at_hotmail.com)
Date: Mon Nov 06 2006 - 14:19:04 CST

Thank you Chris. What about these 3 variables?
dxi
xiMin
xiMax

cheers

>From: Chris Chipot <Christophe.Chipot_at_edam.uhp-nancy.fr>
>To: Ugur Akgun <ugur_iowa_at_hotmail.com>
>CC: namd-l_at_ks.uiuc.edu
>Subject: Re: namd-l: ABF on a single molecule
>Date: Sun, 05 Nov 2006 10:26:53 +0100
>
>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
>_______________________________________________________________________

_________________________________________________________________
Stay in touch with old friends and meet new ones with Windows Live Spaces
http://clk.atdmt.com/MSN/go/msnnkwsp0070000001msn/direct/01/?href=http://spaces.live.com/spacesapi.aspx?wx_action=create&wx_url=/friends.aspx&mkt=en-us

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:19:52 CST