Thanks Justin, those are good points. A quick follow up, would you (or someone else) consider the APL-values I have for my mixed bilayer system to be good, just ok-ish or plain wrong?
THANKS 2013/5/8 Justin Lemkul <jalem...@vt.edu> > > > On 5/8/13 11:09 AM, Gmx QA wrote: > >> 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? >> >> > The .mdp settings are fine as far as I can tell. If you're concerned > about accuracy, you should be analyzing a known system and trying to > reproduce it. There is no reason in my mind why a binary lipid system > should produce the behavior of a pure lipid system. Lipids affect each > other (just like all molecules do). Headgroup interactions and acyl chain > packing get more complex with increasing numbers of different lipids. > > -Justin > > -- > ==============================**========== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<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<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<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
