Re: ABF - zCoord for more than one monomer

From: Chris Chipot (Christophe.Chipot_at_edam.uhp-nancy.fr)
Date: Mon Nov 13 2006 - 07:47:30 CST

Ugur,

> 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

                             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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