Re: ABF - zCoord for more than one monomer

From: Chris Chipot (
Date: Mon Nov 13 2006 - 07:47:30 CST


> 1) I have run a 2.5ns example run, on one monomer with a ligand moving
> in it. Looks like it gives reasonable output.. Now I want to use all
> monomers in my system. How can I use ABF on more than one monomer
> system, at the same time? Is there a way to do it by just modifying the
> input file? Or do I have to modify zCoord.tcl ?

We have not released the multiple-coordinate version of ABF yet. It is
in the pipeline, however, and should happen in the near future.

> 2) I realized that dSmooth should be chosen according to dxi, but is
> there an efficient ratio?

Please, check J. Chem. Phys. 2005, 123, 244906, where different values
of dSmooth and dxi have been explored.

> 3) What should I modify in zCoord input file to use Umbrella Sampling
> along with ABF?

ABF is a method for determining free energy profiles along an order
parameter. Umbrella sampling is another one. Why would one combine
the two? If, however, by umbrella sampling you mean "adding a set of
restraints", please, refer to the user's guide of NAMD, in the section
"Including restraints in ABF simulations".

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 Vandœuvre-lès-Nancy Cedex, France


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

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