Hi Xavier Many thanks for the reply. When I compare the two curves Curve 1) lack of overlap in barrier region; force constant = 1000 Curve 2) with increased number of sampling windows with increased force constant (note I have only increased the force constant of the windows in the barrier region). Force constant =1000, Force constant in barrier region = 5000
The barrier increases due to better sampling in this region (expected), but the rest of the curve in 2) is shifted upward compared to curve 1). Why is this so when the only difference is the increased number of windows and force constant in one region? Gavin XAvier Periole wrote: > > On Jan 5, 2011, at 4:08 PM, Gavin Melaugh wrote: > >> Dear all >> >> I have generated a PMF curve for introducing a guest molecule into a >> host molecule using the umbrella sampling method. The curve seems fine, >> but there are no overlaps between histograms in the barrier region. To >> circumvent this I have added more windows in this region and to ensure >> sampling have increased the force constant only in this region. The >> windows in this problematic region are now not equally spaced. Does this >> matter for g_WHAM? > Nope it does not matter. >> Could someone please reply to me on this matter as it >> has been a sticking point for me for quite sometime? >> >> 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
