[gmx-users] deltaG shifts in g_wham

[Alex]

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?

Thanks,

Alex