I am pulling through the channel with respect to a single residue on one "side"(extracellular) of the structure. I have used pull_geometry = distance & pull_dim = N N Y. From this what I understood is ligand will pull along the z direction with respect to the reference group (away from r_57). (i.e from extracellular to intracellular). Is this correct?
Here is my umbrella sampling .mdp 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_k1 = 1000 pull_init1 = 0 On Mon, May 10, 2010 at 4:50 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Aswathy wrote: > >> Thanks for your reply. >> >> In this case reference (r57) is not the part of the channel. But it is a >> residue in the loop above the channel entry. Thats why I used >> pull_geometry=distance. Therefore I am pulling the ligand away from this >> reference. >> >> > So you are not pulling through the channel? Or you are pulling through the > channel with respect to a single residue on one "side" of the structure? If > your ligand ever crosses over this reference in any way, the reference > distance will change sign and thus Tom is right, you should use > "pull_geometry = position." With "distance," you can only ever have > positive reference distances. > > What are your .mdp settings during umbrella sampling? > > -Justin > > Thanks >> -Aswathy >> >> >> On Mon, May 10, 2010 at 3:05 PM, Thomas Piggot <t.pig...@soton.ac.uk<mailto: >> t.pig...@soton.ac.uk>> wrote: >> >> Hi, >> >> If you defined the reference (r_57) as part of your channel then >> with pull_geometry=distance you will have problems as the distance >> between pull_group1 and pull_group0 becomes closer to zero and then >> the distance becomes positive again. >> >> I recently had this with my umbrella sampling simulations. Search >> for the discussion of things you can do to address this issue on the >> list. To stop this being a problem in the first place you should >> have used pull_geometry=position. >> >> Cheers >> >> Tom >> >> Aswathy wrote: >> >> 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 >> <mailto:ammasa...@gmail.com> <mailto:ammasa...@gmail.com >> >> <mailto: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 <mailto:joc...@xray.bmc.uu.se> >> <mailto:joc...@xray.bmc.uu.se >> <mailto: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 <mailto:gmx-users@gromacs.org> >> <mailto:gmx-users@gromacs.org <mailto: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 >> <mailto:gmx-users-requ...@gromacs.org> >> <mailto:gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org>>. >> >> Can't post? Read >> http://www.gromacs.org/mailing_lists/users.php >> >> >> >> >> -- Aswathy >> >> >> >> >> -- Aswathy >> >> >> -- Dr Thomas Piggot >> University of Southampton, UK. >> >> -- gmx-users mailing list gmx-users@gromacs.org >> <mailto: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 >> <mailto:gmx-users-requ...@gromacs.org>. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> >> >> >> -- >> Aswathy >> >> > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > > -- > 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
-- 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
