Here is also the sample .mdp file chris.ne...@utoronto.ca wrote: > can you show us your mdp and the pmf and the histograms for the data > that you put into wham? It's a lot easier to diagnose with the real data. > > In the general case where umbrellas are spaced equally along your > reaction coordinate, sampling overlap between umbrellas will always > decrease anywhere the PMF is concave down, such as your barrier > region. I would suggest adding windows at every 0.005 nm spanning the > region that you consider to have a sampling problem (e.g. 0.76 to 0.83 > ?) and use a much stronger force constant here (e.g. 2-3 times as > strong as you used for umbrellas with 0.02 nm spacing). You have > identified a problem, so my suggestion is to not bother fiddling with > adding one extra replica but sample that region to death with strong > force constants. I presume that this will not impact your overall > efficiency too much if the reaction coordinate is long overall. > > Finally, you will need to evaluate the convergence of your PMF overall > and perhaps of this region in particular, especially if you want to > know the dG to cross it or between two low energy states on either > side of it. > > Chris. > > -- original message -- > > > Sorry I am not sure that I follow. Will the window with r0 =0.80 giving > the distribution centred around 0.78nm not drive my free energy profile > up. If I remove this window prior to running g_wham the free energy goes > down. Should I increase the force constant so that the mean of the > window is 0.80nm (bearing in mind that this is near the barrier region). > > Gavin > XAvier Periole wrote: >> >> You can present the data differently: >> you have two windows at 0.78 nm giving different distribution. >> >> That indicates these windows are not converged. Does not mean >> that the others (0.80 nm) are converged :)) >> >> On Mar 31, 2011, at 12:20 PM, Gavin Melaugh wrote: >> >>> Hi Xavier >>> >>> Thanks for the reply. With respect to your answer of my first query. >>> What if you had two windows practically on top of each other, but one >>> was not supposed to be there. e.g A window with r0 of 0.80 nm and >>> centred at 0.78 nm and a window with r0 of 0.78 nm centred at 0.78nm. >>> >>> Gavin >>> >>> XAvier Periole wrote: >>>> >>>> On Mar 31, 2011, at 11:53 AM, Gavin Melaugh wrote: >>>> >>>>> Hi All >>>>> >>>>> I have generated several PMF curves for the one system using umbrella >>>>> sampling. In the first part of the curve (barrier region) I use a >>>>> high >>>>> force constant with small intervals between the windows. The latter >>>>> part >>>>> of the curve I use a lower force constant with larger window spacing. >>>>> Anyway I have a few issues that I need clarifying: >>>>> 1 - Can you have too much overlap between windows? >>>> no, there no such a thing of too much overlap :)) You could even put >>>> two identical windows with same 100% overlap ... no problem. >>>>> 2 - Does the distribution at each window have to centered around the >>>>> desired r0? (If not does this affect the free energy?) >>>> The deviation of the distribution from the r0 is what dictates the >>>> profile. The more away from the disired r0 the higher the free energy >>>> of the system. >>>>> 3- If you over sample one particular window, will it affect the >>>>> curve? >>>> There is no such a thing of over sampling ... the only thing you can >>>> have is not enough sampling. >>>>> >>>>> Many thanks >>>>> >>>>> GAvin >>>>> -- >>>>> gmx-users mailing list gmx-users at gromacs.org >>>>> 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 gmx-users-request at gromacs.org. >>>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>> >>> >>> -- >>> gmx-users mailing list gmx-users at gromacs.org >>> 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 gmx-users-request at gromacs.org. >>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >
umbrella114.mdp
Description: application/mdp
-- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
