[gmx-users] PMF changing drastically with the number of bins
Sajeewa Pemasinghe
sajeewasp at gmail.com
Mon Dec 19 10:45:11 CET 2016
Dear all,
I have made mistake. I didn't compare the value of free energy at the
minimum with the plateau value. At all three bin numbers the difference is
close to 2 kCal mol-1.
So this is solved.
Best regards
Sajeewa
On Mon, Dec 19, 2016 at 1:15 PM, Sajeewa Pemasinghe <sajeewasp at gmail.com>
wrote:
> Dear all,
>
> I am calculating the PMF as the COM distance of two molecules are changing
> using umbrella sampling ( pull = umbrella ). Each umbrella sampling
> simulation runs for 50ns. When I calculate the PMF with default (200 bins)
> settings using gmx wham I get the minimum in free energy of -1.19 kCal
> mol-1 at 24.9 Angstrom. When I change the number of bins to 100 the new
> value for minimum is -0.558 kCal mol-1 at 24.8 Angstrom and for 50 bins it
> is -0.195 kCal mol-1 at 24.7 Angstrom. Can the free energy value be this
> much dependent on the number of bins? I suppose the normalization of total
> probability to 1 happens inside the algorithm. Could anyone give me a
> suggestion to this much of a variation?
>
> Best regards
>
> Sajeewa
>
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