Hi Justin, Thanks, that's reassuring then. My reason for worrying was in part because the reported electron densities in several papers I have read seem to match very closely. But since as you say the APL values also agree then everything might be ok after all?
Thanks /PK 2016-02-24 15:52 GMT+01:00 Justin Lemkul <jalem...@vt.edu>: > > > On 2/24/16 7:25 AM, Gmx QA wrote: > >> Dear list >> >> I have a simulation of a system of 64 POPC lipids per leaflet using the >> Charmm36 lipid parameter set, and I am calculating the electron density >> across the bilayer to compare to literature values. Unfortunately I cannot >> quite get the same results as eg. in Klauda et al ( >> http://www.sciencedirect.com/science/article/pii/S0005273614002193) >> >> I have made the starting structure using the charmm-gui, and gone through >> all the equilibration steps as suggested in the gromacs tar-ball from that >> website. >> >> My production mdp file is the following: >> >> integrator = md >> dt = 0.002 >> nsteps = 50000000 >> nstlog = 10000 >> nstxout = 500000 >> nstvout = 500000 >> nstfout = 0 >> nstcalcenergy = 10 >> nstenergy = 1000 >> nstxtcout = 500000 >> ; >> cutoff-scheme = Verlet >> nstlist = 20 >> rlist = 1.2 >> coulombtype = pme >> rcoulomb = 1.2 >> vdwtype = Cut-off >> vdw-modifier = Force-switch >> rvdw_switch = 1.0 >> rvdw = 1.2 >> ; >> tcoupl = Nose-Hoover >> tc_grps = POPC SOL >> tau_t = 1.0 1.0 >> ref_t = 303.15 303.15 >> ;nsttcouple = 1 >> ; >> pcoupl = Parrinello-Rahman >> pcoupltype = semiisotropic >> tau_p = 5.0 5.0 >> compressibility = 4.5e-5 4.5e-5 >> ref_p = 1.0 1.0 >> ; >> constraints = h-bonds >> constraint_algorithm = LINCS >> continuation = yes >> ; >> nstcomm = 10 >> comm_mode = linear >> comm_grps = POPC SOL >> ; >> refcoord_scaling = com >> >> Simulations are run with gromacs 5.0.4, and currently 100 ns long. >> >> Before running vmx density, I center my trajectory like this: >> $ gmx trjconv -f run.trr -s em.tpr -o run_center.trr -center >> >> selecting POPC as the group to center on. >> >> Then, my command for computing the electron density is the following >> (also >> using gmx density 5.0.4): >> >> $ gmx density -f run_center.trr -s em.tpr -o density_traj_center.xvg >> -dens >> electron -ei electrons.dat -center >> >> Again, selecting POPC to center the density profile on. >> >> The resulting profile can be found here (i hope that works) >> http://www.filedropper.com/compareelectrondensity >> >> As you can see, the depth of the central trough is not as deep as the >> literature value, nor is the height of the density the same even though >> the >> peak-peak distance appears to be similar, and values in the other regions >> also match _fairly_ closely. >> >> The average APL value over the entire trajectory is 64.0 +- 1.33, which is >> in line with the reported 64.7 from Klauda, but the electron density >> worries me a bit. Perhaps anyone (Justin?) can shed any light on this? >> >> > Why? The results match almost perfectly. The magnitude of error is > within a few % and if your APL matches then I'm sure everything is fine. > We rigorously tested the lipid inputs, cutoff setup, etc. and everything > agrees quite well between lipid simulations in CHARMM, GROMACS, AMBER, > NAMD, and OpenMM. There are minor variations, as would be expected in > comparing any two software programs, but nothing is really aberrant. > > http://dx.doi.org/10.1021/acs.jctc.5b00935 > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.