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

From: Chris Chipot (
Date: Tue Dec 20 2005 - 01:28:32 CST


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


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

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