Re: ABF restrain

From: Chris Chipot (
Date: Wed Jul 04 2007 - 17:17:41 CDT


if what you are interested in is generating a PMF with ABF, then
the use of the word "restraint" here is inappropriate.

Your RC can be defined as "zCoord-1atom", where abf1 corresponds
to a list of reference atoms of the channel and abf2 is your K+
ion. This RC is the distance separating the COM of your reference
set of atoms from the ion projected onto the z axis, presumably
the normal to the water-membrane interface.

If you want to measure the change in free energy between 3 and 6
angstroms, then you ought to set XiMin and XiMax to the corresponding

Chris Chipot

alex digenova bravo a écrit :
> Hi all
> Im am using ABF for calculate the PMF of an ion (k+) in a channel, So
> I am interested in restrain my ion at my RC for examples between 3 to
> 6 in axis Z. what kind of restrain can I use?
> Thank you
> good bye
> Alex Di Génova Bravo.

Chris Chipot, Ph.D.
Equipe de dynamique des assemblages membranaires
Unité mixte de recherche CNRS/UHP No 7565
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