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 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? Thanks, Dejun -- 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
