ABF - zCoord for more than one monomer

From: Ugur Akgun (ugur_iowa_at_hotmail.com)
Date: Thu Nov 09 2006 - 10:19:47 CST

Dear All;
I m new using ABF, looks like my system works, now I am trying to improve
it, I have few questions, and appreciate any help..

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 ?

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

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


>From: "Ugur Akgun" <ugur_iowa_at_hotmail.com>
>To: Christophe.Chipot_at_edam.uhp-nancy.fr
>CC: namd-l_at_ks.uiuc.edu
>Subject: Re: namd-l: ABF on a single molecule
>Date: Mon, 06 Nov 2006 16:33:24 -0600
>Thanks a lot Chris;
>I had a little difficulty to understand how to use the different types of
>abf coordinate fies.
>I think it is working now, I'll check the results and get back to you...
>>From: Chris Chipot <Christophe.Chipot_at_edam.uhp-nancy.fr>
>>To: Ugur Akgun <ugur_iowa_at_hotmail.com>
>>CC: namd-l_at_ks.uiuc.edu
>>Subject: Re: namd-l: ABF on a single molecule
>>Date: Mon, 06 Nov 2006 22:19:17 +0100
>>This is all spelled out in the NAMD user's guide. For additional
>>details, please, check out J. Chem. Phys. 2004, 121, 2904–2914
>>and J. Chem. Phys. 2005, 123, 244906.
>>Ugur Akgun a écrit :
>>>Thank you Chris. What about these 3 variables?
>>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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