Thank you very much for your help. I've run my simulations for 80 ns. I will add more windows along the reaction coordinate.
Thank you, Susana On Tue, Feb 15, 2011 at 2:56 PM, Justin A. Lemkul <[email protected]> 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. > > -Justin > > > Thank you in advance, >> >> Susana >> >> > -- > ======================================== > > 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> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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