[gmx-users] deltaG shifts in g_wham

[Justin Lemkul]

On 6/7/17 4:18 PM, Alex wrote:
> Hi all,
> 
> I am using 'gmx wham' (GMX 5.0.4) on a system that consists of a membrane
> with a narrow pore and an ion. The configurations correspond to various
> heights "above" the membrane (0 to 1.5 nm).
> 
> In one case, the ion is K+, in another Na+. In both cases the results are
> fairly reasonable, but there is a bit of a numerical caveat.
> 
> For sodium, the free energy away from the pore is close to zero and
> considerably negative inside the pore, as one might expect. For potassium
> (the input files are nearly identical), the free energy far away from the
> pore is a considerable _positive_ value and zero inside the pore. I do
> realize that absolute values are meaningless and I can always "shift" the
> results to correspond to near-zero far away from the reactive site (and
> when I do, I even have reasonable agreement with experiment). However, I
> want to understand what is happening with the utility. My simulation times
> are quite moderate (1 ns for each config).
> 
> Can someone help?
> 

WHAM sets the "left-most" window (i.e. smallest value of zeta) to zero and 
calculates all free energy values relative to that.  This is why you can offset 
at any given point.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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