Re: NAMD 2.7b1 ABF + free energy windows

From: Jerome Henin (jhenin_at_cmm.chem.upenn.edu)
Date: Wed Sep 30 2009 - 04:44:58 CDT

Hi David,
Giovanni's advice will work with ABF from NAMD 2.6. If you use the
colvars module in NAMD 2.7, the simplest way to integrate is to
concatenate the gradient files (*.grad) and integrate the complete
data set numerically.
Jerome

2009/9/30 Giovanni Bellesia <gbellesia_at_chem.ucsb.edu>:
> I forgot,
> you also have to modify the values of xiMin and xiMax to "cover" the whole
> range of your "order parameter"
>
> Hi,
>
> Hopefully someone can point what Iím missing or the mistake Iím making. Iím
> 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. Iíve broken
> the simulation down into three windows of approximately 10 angstroms over 2
> ns, and theyíve all successfully completed. The sampling could definitely be
> improved but itís enough for some comparisonís Iím looking at. Hereís the
> problem when I plot A(xi) vs Xi for each of these windows, they donít match
> up. In the overlaps between windows the plots look the same but theyíre
> 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, shouldnít 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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