Can any one help me please? I looking forward to hear from any of you. Thank you.
On Thu, May 6, 2010 at 1:19 PM, Aswathy <ammasa...@gmail.com> wrote: > 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 at 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. How can we > get increased PMF even when the ligand is reached out of the channel? > > Did I made any mistake any where , I am confused. > > 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 > -- Aswathy
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