Re: NAMD 2.7b1 ABF + free energy windows

From: Giovanni Bellesia (gbellesia_at_chem.ucsb.edu)
Date: Tue Sep 29 2009 - 16:57:15 CDT

Hi,
I think you have to add a final step to your calculation, i.e., you have
to run a final simulation (which could be just 0 timesteps) and add the
following two lines in your config file:

abf outFile final.abf
abf inFiles {1.abf 2.abf 3.abf}

where 1.abf 2.abf and 3.abf are the three files generated from your
previous simulations over the three windows.
You should find the "continuous" free energy profile in final.abf

A final note: this is what I understood going through the mailing list.
It worked perfectly for my calculations (I had to "connect" 10 different
windows).

Giovanni

> Hi,
>
> Hopefully someone can point what I'm missing or the mistake I'm
> making. I'm using ABF to calculate the free energy of a steroid moving
> from the center of a lipid bilayer into bulk water over a range of 28
> angstroms. I've broken the simulation down into three windows of
> approximately 10 angstroms over 2 ns, and they've all successfully
> completed. The sampling could definitely be improved but it's enough
> for some comparison's I'm looking at. Here's the problem when I plot
> A(xi) vs Xi for each of these windows, they don't match up. In the
> overlaps between windows the plots look the same but they're offset on
> the y-axis in one case by 3 kcal/mol, and in the other by 15 kcal/mol.
> Am I missing something here, shouldn't the plots match up ?
>
> Thanks in advance,
>
> -david
>
> David E. Reichert, PhD.
>
> Asst. Professor of Radiology
>
> Washington University School of Medicine
>
>
>
> e-mail: reichertd_at_wustl.edu
>
> voice: 314-362-8461
>
> fax: 314-362-9940
>
> web: http://scoobie.wustl.edu/
>
>
>
>
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-- 
------------------------------------------
Giovanni Bellesia
Department of Chemistry and Biochemistry
University of California, Santa Barbara
Santa Barbara, California 93106-9510, USA.
Email: gbellesia_at_chem.ucsb.edu
Phone: 805 893 2767
Web: http://www.chem.ucsb.edu/~gbellesia/
------------------------------------------

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