I am doing US . Yes, histograms of population densities along the reaction coordinate. Please find the pull settings. Sampled for 800ps.(nsteps = 400000). Pull_init will vary for each frame, depends on the window spacing.
pull = umbrella pull_geometry = position pull_dim = N N Y pull_start = no pull_nstxout = 10 pull_nstfout = 10 pull_ngroups = 1 pull_group0 = U_ref pull_pbcatom0 = 0 pull_group1 = r_C1 pull_pbcatom1 = 0 pull_init1 = 0 0 0.1 pull_k1 = 1000 pull_rate1 = 0 pull_vec1 = 0 0 0 Please check this link for my histograms https://docs.google.com/fileview?id=0B1PyTWWGrqt6MDU3NWYwMGUtNjY5Zi00NDBmLWE0YzMtYTNjODVlOGFlNWVl&hl=en I would greatly appreciate our suggestions. Thank you, -Aswathy On Mon, Jun 21, 2010 at 8:14 PM, <chris.ne...@utoronto.ca> wrote: > Please clarify: > > Are doing SMD or are you doing US? If you're doing SMD then you should not > be using WHAM and you should not really be able to generate any sampling > histograms. > > Are the histograms that you are referring to population densities of the > sampling along your reaction coordinate? > > My guess -- if you're doing US -- is that you have some incorrect pull > group settings. Bimodal distributions are indeed possible, but should > require very long sampling times to achieve, and I doubt that you are at > those times yet. Your Fc is fine. Post your pull settings. > > Chris. > > -- original message -- > > When i did the Umbrella sampling of frames from an SMD (of ligand > transport), I am getting bimodal histograms in some cases. > > Do you think this is because , the force constant that i used is very low > (i > used pull_k1=1000).? Are these bimodal peaks may cause any deviation in my > PMF result? Do I need to repeat the sampling again with another pull_k1 > value(higher value)? > > > > -- > 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/search before posting! > Please don't post (un)subscribe requests to the list. Use thewww interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Aswathy
-- 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/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/mailing_lists/users.php
