Hi gmx-users, I've been experimenting with simulations of mixed bilayers (512 lipids in total, 70% POPC, 30% POPE) using the charmm36 parameter set in gromacs, and have a couple of questions. I know this has been discussed before, but I'd appreciate some input nonetheless :-)
The relevant sections of my mdp-file are pasted below: ; Start time and timestep in ps tinit = 0 dt = 0.001 nsteps = 100000000 ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = 5 ; ns algorithm (simple or grid) ns_type = grid ; Periodic boundary conditions: xyz, no, xy pbc = xyz periodic_molecules = no ; nblist cut-off rlist = 1.2 ; long-range cut-off for switched potentials rlistlong = 1.4 ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = PME rcoulomb-switch = 0 rcoulomb = 1.2 ; Relative dielectric constant for the medium and the reaction field epsilon_r = 1 epsilon_rf = 1 ; Method for doing Van der Waals vdw-type = switch ; cut-off lengths rvdw-switch = 0.8 rvdw = 1.2 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = No ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling tcoupl = V-rescale nsttcouple = -1 nh-chain-length = 10 ; Groups to couple separately tc-grps = System ; Time constant (ps) and reference temperature (K) tau_t = 0.1 ref_t = 300 ; Pressure coupling pcoupl = Parrinello-Rahman pcoupltype = semiisotropic nstpcouple = -1 This is as far as I can tell from earlier discussions on the list, and also from reading the Piggott et al. paper in JCTC, the correct settings for charmm36. After a simulation of ~50 ns, I use GridMatMD to calculate the area per headgroup of POPC and POPE, respectively, and get what I think are not 100% acceptable results (but maybe they are) For POPC, I get 59,7 A^2, and for POPE, I get 63,1 A^2. The value for POPE would have been fine I suppose if it hadn't been for the fact that the APL for POPC is smaller. Should it not be larger than POPE? I notice in the Piggott-paper that they in the supplement for some simulations of POPC also get APL's of around 59-60 (without POPE of course), and that the results depend to some extent also on the usage of TIP3P vs TIP3SP water models. I have been using "normal" TIP3P here. Could anyone comment on (a) my mdp-file settings, and (b) the resulting APL, and tell me if I should be worried about anything? THANKS -- 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
