[gmx-users] Umbrella sampling windows
susietomasio at gmail.com
Tue Feb 15 16:19:02 CET 2011
Thank you very much for your help.
I've run my simulations for 80 ns.
I will add more windows along the reaction coordinate.
On Tue, Feb 15, 2011 at 2:56 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> 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 the calculations.
> 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 more.
> Thank you in advance,
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | <+15402319080>(540) 231-9080 <+15402319080>
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