Ok i will explain you in detail. Initially i pulled the ligand through the protein channel , using the given parameters.
pull = umbrella pull_geometry = distance pull_dim = N N Y pull_start = yes pull_nstxout = 10 pull_nstfout = 10 pull_ngroups = 1 pull_group0 = r_57 pull_group1 = r_C1 pull_rate1 = 0.01 pull_k1 = 1500 Then I extracted the frames from the trajectory using the perl program provided with tutorial. COM distance I took as nearly 0.12 nm. (But sometimes I failed to obtain frames exactly at that interval, but took nearly 0.12). Each frame I used for Umbrella sampling for 1ns. Then I checked histograms for overlapping (Some histograms were entirely overlapped and I removed that from the list, where ever gaps i selected new frames and did sampling so that I can get an evenly distributed histograms , I know this will change the overall COM distribution but is there any other way to solve this?) . Finally once I obtained reasonably good overlapped histograms, I plotted PMF using g_wham. The plot was a steeply increasing potential with some small curves here and there. The PMF is not at all converged. Did I made any mistake any where , I am confused. If you want I can attach the PMF profile Thank you. -Aswathy On Thu, May 6, 2010 at 12:56 PM, Jochen Hub <joc...@xray.bmc.uu.se> wrote: > Aswathy wrote: > >> >> Hi gromacs users, >> >> I am using Gromacs 4.0.4 package. I am doing SMD of a ligand transport >> through a channel. >> >> I performed SMD and did umbrella sampling (Thanks to Justin for his >> tutorial). Extracted frames with a window spacing interval of ~0.12nm. and >> did 1ns sampling. Histograms are with reasonabvle overlap. Then I used >> g_wham for plotting PMF considering first 300ps as equilibration. >> > Isn't SMD usually referred to pulling at some finite pulling speed? That > would not be umbrella sampling. > > Anyway, you'll have to provide a lot more data to enable us to help you. > > Jochen > > > > >> I am getting a plot , but potential is increasing constantly. ie, PMF is >> not converged as mentioned the tutorial? Do I need to extend the sampling ? >> or any other reason? >> >> Please help me. >> Thank you. >> >> -Aswathy >> > > > -- > --------------------------------------------------- > Dr. Jochen Hub > Molecular Biophysics group > Dept. of Cell & Molecular Biology > Uppsala University. Box 596, 75124 Uppsala, Sweden. > Phone: +46-18-4714451 Fax: +46-18-511755 > --------------------------------------------------- > > -- > 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 > -- Aswathy
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