[gmx-users] Umbrella sampling windows
Justin A. Lemkul
jalemkul at vt.edu
Tue Feb 15 15:56:46 CET 2011
Susana Tomasio wrote:
> Hi all,
> I'm running umbrella sampling of an ion through a lipid bilayer with
> gromacs 4.5.1.
> I used g_wham to create the histograms of the configurations within the
> umbrella sampling windows (1 Angstrom interval).
> I did not get a sufficient overlap between the windows, so I was
> wodering which is the better way of increasing the sampling: to
> include additional windows in the regions where there is no overlap or
> to increase the force constant ?
If you increase the force constant, you will make the distributions narrower,
and thus I would expect the overlap would be worse. Insufficient simulation
length could be an issue, too, but you haven't said how long your simulations are.
> If I increase the force constant can I continue the simulation with the
> new constant or do I have to start again?
You'd have to start over again, I'd think, otherwise if you pass one .tpr file
to g_wham per window, it will contain incorrect information that will mess up
> I used a force contant of 3000 kJ mol^-1 nm^-2.
That seems somewhat high, but there are no hard and fast rules about these
things, I don't think. You probably want either (1) a lower force constant or
(2) more windows along your reaction coordinate. Option (2) seems to be more
efficient, since you don't have to re-do your simulations, you can just run some
> Thank you in advance,
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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