Hi Xavier Many thanks. Two more quick questions (both refering to barrier region): Does the value of the force constant affect the height of the barrier providing that there is reasonable overlap? Obviously there is a compromise between the size of the constant and the number of windows. If I increase the force constant and number of windows to obtain a high density of sampling, does this give a more accurate curve?
Gavin XAvier Periole wrote: > > On Jan 5, 2011, at 5:01 PM, Gavin Melaugh wrote: > >> 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? > the relative position of the regions on the left and right of your > "barrier" > region is completely depending on the barrier region! > > you may have overestimated the difference between bound/unbound states > because the energy barrier region was not sampled. > > Note also that cure one is simply wrong so comparing to it is dangerous. > > You have to be careful that you might still not have a converged > sampling: > you might have overlap of your histograms on the reaction coordinate but > other degrees of freedom are not fully sampled ... that might result in a > funny and wrong profile. You might want to look at your simulations for > funny things ... > >> >> 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 > -- 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
