4. you could even try NVT ensemble 2016-08-18 2:25 GMT+08:00 li he <parachuternewy...@gmail.com>:
> 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.