Re: define abf1 and abf2 for CM of water and CM of molecule

From: Manori Indira Jayasinghe (manori_at_physics.uc.edu)
Date: Wed Dec 21 2005 - 11:26:37 CST

Dear Chris,

Thank you very much for the Tcl script for abf1. The Abf code is running
and. I have a question.Do I need to on the biasing force. I put it off
anf it gave me a warning

"TCL:
ABF> *****************************************************
TCL: ABF> *** WARNING --- Biasing force will NOT be applied ***
TCL: ABF> *****************************************************
. I have attached my abf script. I would greatly appeciate if you could
check the script and put your comments before i use it for production
runs. Thank you very much.
 On Tue, 20
Dec
2005, Chris Chipot wrote:

> Manori:
>
> in the following example, the reaction coordinate is the distance
> separating the COM of a small, 13-atom solute (abf2) and the COM
> of a water lamella made of 800 water molecules:
>
> abf coordinate zCoord
>
> abf abf2 {1 2 3 4 5 6 7 8 9 10 11 12 13}
> set water 14
> for {set n 1} {$n <= 800} {incr n}
> {append water " [expr 14 + $n * 3 ]"}
> abf abf1 $water
>
> It is necessary to define an intermediate variable, water, and
> assign to the latter the index of the oxygen atom of the first
> water molecule, i.e. 14. Next, the for-loop defines the list of
> water oxygen atoms to which the counter-average force will be
> applied (if an average force is exerted on the COM of the solute,
> then, necessarily, a counter-force should be applied to the water
> lamella). Last, abf1 is defined as the list of water oxygen atoms.
>
> Note that inclusion of all atoms in the computation of the solute
> COM is not a prerequisite. It may be done from subsets of atoms,
> but you ought to remember that your reaction coordinate should be
> fully decoupled from constrained degrees of freedom.
>
>
> Chris Chipot
>
> _______________________________________________________________________
>
> 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
>
> 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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