I see. That makes things clear. Thank you so much! -Dejun ________________________________________ From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul [jalem...@vt.edu] Sent: Thursday, May 26, 2011 1:09 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] To get PMF using pull geometry of cylinder
Lin, Dejun wrote: > Ah...Sorry if I confused you. Actually what I meant is if I set the pull > code, e.g., as: > pull_geometry = position > pull_dim = N N Y > pull_rate1 = 0.1 > pull_init1 = 3.0 > pull_vec1 = 0 0 1 > (where pull rate is NOT zero) > Then the position = pull_init + time*pull_rate*pull_vec1 and since pull_vec1 > is z-component-positive (0, 0, 1), the position between the reference and the > pull group increases monotonically and that's not what I want. I want the > distance to decrease so the pull_vec1 should be (0,0,-1). Am I right? > If you want the two species to approach rather than separate, do not change the pull_vec, change the pull_rate so that it is less than zero. A negative pull_rate will decrease the separation over time. Note that pull_dim is irrelevant for pull_geometry=position; only pull_vec1 is required. -Justin > Thanks, > Dejun > > ________________________________________ > From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf > Of Justin A. Lemkul [jalem...@vt.edu] > Sent: Thursday, May 26, 2011 11:26 AM > To: Discussion list for GROMACS users > Subject: Re: [gmx-users] To get PMF using pull geometry of cylinder > > Lin, Dejun wrote: >> Thank you Justin. But I'm still confused about the pull_vec1. Is the vector >> pointing from the reference or from the pull group for all the geometry >> settings? For instance, if I use pull_geometry = position, pull_dim = N N Y, >> pull_rate1 = 0.1, pull_init1 = 3.0, pull_vec1 = 0 0 1, the position = >> pull_init + time*pull_rate*pull_vec1 according to the manual and it's >> actually pulling the pull group away from the reference because the vector >> has a positive z component. >> > > The reference group serves as the reference :) Thus, the vector connecting > your > reference and pull group is (0,0,1) since the pull group has a larger > z-coordinate. You're right about the position equation, but you've got a > pull_rate1 of zero, so the added term drops out and position = pull_init1. > >> BTW, I did consider using position geometry but can I get the PMF using >> pull_rate NOT equal to zero? The reason I turned to cylinder is that with >> "distance" geometry the membrane concaved as the micelle was restrained to a >> very short distance (any distance below the critical distance where the >> fusion was supposed to occur) without fusing and this would persist for some >> hundred nanoseconds. >> > > To obtain the PMF, the pull rate should be zero, using several (many) > independent simulations along the desired reaction coordinate. See the > tutorial: > > http://www.gromacs.org/Documentation/Tutorials#Pull_Code_and_Umbrella_Sampling > > -Justin > >> Thanks again for your help! Dejun >> >> ________________________________________ From: gmx-users-boun...@gromacs.org >> [gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul >> [jalem...@vt.edu] Sent: Wednesday, May 25, 2011 7:44 PM To: Discussion list >> for GROMACS users Subject: Re: [gmx-users] To get PMF using pull geometry of >> cylinder >> >> Lin, Dejun wrote: >>> Hi all, >>> >>> I want to do an umbrella sampling to calculate the potential of mean force >>> of a micelle fusing to a lipid membrane. In the starting configuration, the >>> membrane normal is set in z direction and the membrane is under the >>> micelle (z(COM-membrane) < z(COM-micelle)). At the beginning, I used >>> pull_geometry = distance but the sampling took to long to converge. And >>> then I considered using cylinder instead and set up the pull code as: pull >>> = umbrella pull_geometry = cylinder pull_dim = N N Y pull_start = >>> no pull_ngroups = 1 pull_group0 = membrane pull_group1 = micelle >>> pull_vec1 = 0.0 0.0 -1.0 pull_r1 = 2.3 pull_r0 = 2.5 pull_init1 >>> = 1.8 pull_rate1 = 0.0 pull_k1 = 1000 pull_nstxout = 1000 >>> pull_nstfout = 1000 >>> >>> And the output files (px.xvg and pf.xvg) look like: (px.xvg) 0.0000 >>> 23.3397 4.90267 100.0000 0.742426 1.86002 >>> 200.0000 0.737842 1.86232 300.0000 >>> 0.762641 1.83985 400.0000 21.6814 >>> 1.86777 500.0000 0.771017 1.82482 600.0000 >>> 0.789036 1.83254 700.0000 0.793745 >>> 1.83503 800.0000 0.804732 1.84217 900.0000 >>> 0.80137 1.84166 1000.0000 0.817979 1.83546 >>> 1100.0000 0.806272 1.83535 1200.0000 0.792355 >>> 1.80372 1300.0000 0.786839 1.8438 1400.0000 0.798686 >>> 1.82625 1500.0000 0.802859 1.84138 1600.0000 0.803844 >>> 1.84379 >>> >>> (pf.xvg) 100.0000 -480.158 200.0000 -498.547 >>> 300.0000 -318.839 400.0000 -542.14 500.0000 >>> -198.526 600.0000 -260.291 700.0000 -280.22 >>> 800.0000 -337.385 900.0000 -333.317 1000.0000 -283.644 >>> 1100.0000 -282.761 1200.0000 -29.7684 1300.0000 -350.409 1400.0000 >>> -209.991 1500.0000 -331.029 1600.0000 -350.309 >>> >>> And I visualized the trajectory in VMD and found that an "explosion" of the >>> micelle (with all its residues scattered in the box). I then changed the >>> pull_vec1 = 0.0 0.0 -1.0 to pull_vec1 = 0.0 0.0 1.0 and the "explosion" >>> was gone and everything seemed to work. But I'm not quite sure if I'm >>> setting up the pull-code right because if z(COM-membrane) < z(COM-micelle), >>> then pull_vec1 = 0.0 0.0 -1.0 should be the right choice. Basically, I >>> think my >> The negative is incorrect. If the micelle is "above" the membrane (i.e., it >> has a greater z-coordinate), then the reference vector should be positive >> with respect to the reference position. It would appear from the pullx.xvg >> file that you've got some weird PBC crossing going on, since the reference >> positions oscillate dramatically at the beginning of the simulation. >> >>> pull-code is restraining the COM of the micelle to the COM of a "cylinder" >>> of the membrane at a distance of 1.8nm, with the vector pointing from >>> COM(micelle) to COM(cylinder) being (0,0,-1). So can anyone explain what >>> caused the explosion or am I setting up the pull-code right? And what are >>> the 2nd and 3rd column in the px.xvg output in this case? >>> >> For such a simple restraint, I don't think there is any need for cylinder >> geometry. You're not using different weighting. Any of the other >> pull_geometry settings should work, with "distance" probably being the most >> intuitive. I suspect it would be very easy to use the "position" setting as >> well. >> >> The output in the pullx.xvg file should be labeled in the header. The >> generic output is (x,y,z) of the reference group, followed by delta(x,y,z) >> for the restrained group, i.e. how far away the restrained group is along >> each coordinate axis. If you're only restraining/pulling along the z-axis, >> then the only terms written are z and dz, since, in principle, x, y, dx, and >> dy are all fixed, with the last two terms being zero. >> >> -Justin >> >> -- ======================================== >> >> 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/Support/Mailing_Lists/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/Support/Mailing_Lists >> > > -- > ======================================== > > 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/Support/Mailing_Lists/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/Support/Mailing_Lists > -- ======================================== 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- 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/Support/Mailing_Lists/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? 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