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 [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 >>> >> >> -- >> 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 > -- 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
