Thanks Justin for the reply Gavin
Justin A. Lemkul wrote: > > > Gavin Melaugh wrote: >> 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). >> > > If you have an incomplete or otherwise discontinuous free energy > profile, then you won't get a correct result, but it's not simply due > to "oversampling" one region. It's that the "oversampling" results in > "undersampling" another region. Increasing the force constant for the > window centered around 0.80 nm should work. > > -Justin > >> 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@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 >>>> -- >>>> 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 >> > -- 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
