Hi All, This is the first time we use Martini force filed and CG polarizable water model. So we decide to repeat the result in the recent published paper. Title: Polarizable Water Model for the Coarse-Grained MARTINI Force Field link: http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000810 We use Gromacs version 4.6-beta3, single precision. we want to repeat figure 9 in this paper, the polarizable martini sodium result.
We build a system containing 128 DPPC, 1 NA+, 1CL-, 2000 CG polarizable water, and we equilibrate the system for about 500ns. The area per lipid we got is around 0.635 nm2. it is the same value reported in the paper. The number density of different cg groups of DPPC and water also match the density reported in the paper. Then we set up 40 windows to compute the pmf of translocation of NA+ through a DPPC bilayer, by using umbrella sampling method. To set up each window, we place sodium ion at the ideal place and turn off the interaction between sodium and other beads in the system , then we slowly grow in the vdw interactions between sodium and the the rest of the system in 10 ns, after that we grow in the vdwq interaction in the same way. The results is shown in this figure. http://udel.edu/~yuanhu/pmf-plos-repeat.png see the mdp file, and log file of the center of bilayer window: http://udel.edu/~yuanhu/tau-us.mdp http://udel.edu/~yuanhu/us.mdp(grompp output mdp file) http://udel.edu/~yuanhu/us.log We add the umbrella sampling code to the end the example mdp file from this website ( http://md.chem.rug.nl/cgmartini/images/parameters/exampleMDP/old/martini_v2.P_example.mdp), it's also the same mdp file shown in the supporting information of this paper. =============================== ; Pull code pull = umbrella pull_geometry = distance pull_dim = N N Y pull_start = no pull_ngroups = 1 pull_group0 = DPPC pull_group1 = NA+ pull_init1 = 0.9 pull_rate1 = 0.0 pull_k1 = 400 ld_seed=-1 =============================== In order to match the PMF, we tried several test, but all of the tests give the similar results. The systems we have tested are as follow: a. T=320k, tau_p=1.0, tau-t=1.0, nstlist=10, rlist=1.2,compressibility=3e-4, tc-grps=DPPC PW_ION h. T=323k, tau_p=5.0, tau-t=1.0, nstlist=10, rlist=1.2,compressibility=3e-4, tc-grps=DPPC PW_ION i. T=323k, tau_p=5.0, tau-t=1.0, nstlist=5, rlist=2,compressibility=3e-4, tc-grps=DPPC PW_ION j. T=323k, tau_p=3.0, tau-t=0.3, nstlist=5, rlist=2,compressibility=3e-4, tc-grps=DPPC PW_ION k. T=323k, tau_p=3.0, tau-t=0.3, nstlist=5, rlist=2,compressibility=4.5e-5, tc-grps=DPPC PW_ION l. T=323k, tau_p=3.0, tau-t=0.3, nstlist=5, rlist=2,compressibility=4.5e-5, pull_vec1= 0 0 1 o. T=323k, tau_p=3.0, tau-t=0.3, nstlist=5, rlist=2,compressibility=4.5e-5,comm-grps= DPPC PW_ION p. T=323k, tau_p=3.0, tau-t=0.3, nstlist=5, rlist=2,compressibility=4.5e-5,tc-grps=DPPC_ION PW q. T=323k, tau_p=3.0, tau-t=0.3, nstlist=5, rlist=2,compressibility=4.5e-5,comm-grps= DPPC PW_ION, tc-grps=DPPC PW ION s. T=323k, tau_p=3.0, tau-t=0.3, compressibility=4.5e-5, comm-grps= DPPC PW ION, tc-grps=DPPC PW ION r. T=325k, tau_p=3.0, tau-t=0.3, nstlist=5, rlist=2,compressibility=4.5e-5,comm-grps= DPPC PW_ION we also tried to use gromacs 3.3.1 version (single precision), but the pmf didn't match either. We don't know where is the problem. We run out of ideas now. Could someone help us? Thanks. -- gmx-users mailing list [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
