I think you could try following things to see if you could get 'better' results 1. use time step of 0.2 or even 0.1 fs 2. try different tau-t and tau-p, e.g. use larger tau-t 3. try different p-coupling methods
2016-08-17 23:28 GMT+08:00 Diez Fernandez, Amanda < amanda.die...@imperial.ac.uk>: > Dear Gromacs users, > > I was trying to reproduce the published values for the diffusion > coefficient of SPCFw water (2.3 +/- 0.08 x 10^-9 m^2/s )before using it in > some of my simulations and I am failing to do so. > More worryingly I get different results for different identical runs. > I am using a 2nm side cubic cell containing 221 water molecules and a time > step of 0.5fs (larger timestep results in a warning since I am not applying > any constraints). > I ran 6 identical simulations (only difference is the random initial > velocities) and I got these different values and error magnitudes. > The trajectories are 10ns long. I discarded the first 2ns for the msd > calculation. > > Nth Simulation Diffusion Coefficient (x 10^-9 m^2/s) > > 1 2.95 +/- 0.071 > 2 2.71 +/- 0.158 > 3 2.52 +/- 0.007 > 4 2.96 +/- 0.26 > 5 2.62 +/- 0.07 > 6 2.71 +/- 0.158 > > Is it normal that I get different results like this? (Despite averaging > over more than 7ns and 221 molecules?). > > Many thanks in advance. Below are the detailed parameters. > > Amanda > > Detailed parameters: > > nstlist = 10 > > ns_type = grid > > rlist = 0.9 > > coulombtype = PME > > rcoulomb = 0.9 > > fourierspacing = 0.12 > > pme_order = 4 > > ewald_rtol = 1e-6 > > vdw-type = cut-off > > rvdw = 0.9 > > pbc = xyz > > tcoupl = nose-hoover > > tc_grps = SYSTEM > > tau_t = 0.4 > > ref_t = 298 > > nsttcouple =-1 > > nh-chain-length = 1 > > pcoupl = Berendsen > > pcoupltype = isotropic > > tau_p = 10.0 > > compressibility = 4.5e-5 > > ref_p = 1.01325 > > refcoord-scaling = all > > DispCorr = EnerPres > > gen_vel = yes > > gen_temp = 293 > > gen_seed = -1 > > constraints = none > -- > 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.
