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?
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 -- 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
