On Mon, May 10, 2010 at 6:29 PM, Justin A. Lemkul <jalem...@vt.edu> wrote:
> Ok . Now I understood. I have one more doubt , as I mentioned to you, I am > using one residue in the extracellular loop as a reference point. Since this > is in the loop, do you think it can be good reference point (due to th large > fluctuatuion in the loop, will it affect the result)? > > Aswathy wrote: > >> 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? >> >> > I don't think so. If you are pulling through a channel, using an > extracellular residue as a reference, you will be changing the sign of the > distance, rendering "pull_geometry = distance" useless. For example, in > order to properly calculate the PMF, you have to pull from the aqueous > solvent, into the channel, then back out into the solvent. At some point, > your ligand is outside the channel (such that, for example, the z-coordinate > of the ligand is greater than that of r_57, so distance > 0). Then, as your > ligand enters the channel, its z-coordinate is less than that of r_57, so > distance < 0. If this is the case, you must use "pull_geometry = position" > to get the correct signs, otherwise your umbrella sampling window reference > distances will be nonsensical. > > -Justin > > 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<mailto: >> 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> >> <mailto: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>> >> <mailto: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>> >> <mailto: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>> >> <mailto: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>> >> <mailto: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> >> <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/searchbefore >> 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 >> >> >> -- ======================================== >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> MILES-IGERT Trainee >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080 >> >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> >> -- 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
