Dear gmx-users, I’m having some problems trying to understand anomalous diffusion coefficient values calculated with g_msd. MSD was calculated for two box with a run of 100ns using these settings
integrator = md tinit = 0 dt = 0.002 nsteps = 50000000;1ns comm-mode = Linear nstcomm = 10 comm-grps = System nstxout = 0 nstvout = 0 nstfout = 0 nstlog = 1000 nstenergy = 80 nstxtcout = 750 xtc-precision = 1500 xtc-grps = System energygrps = NAP NA WAT MET SI3 SI- I LI+ LI- nstlist = 20 ns_type = grid pbc = xyz periodic_molecules = no rlist = 0.9 coulombtype = PME rcoulomb = 0.9 vdw-type = Cut-off rvdw = 1.0 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 6 ewald_rtol = 1e-5 optimize_fft = yes Tcoupl = v-rescale tc-grps = NAP NA WAT MET SI3 SI- I LI+ LI- tau_t = 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 ref_t = 298 298 298 298 298 298 298 298 298 Pcoupl = Parrinello-Rahman Pcoupltype = Isotropic tau_p = 1 compressibility = 4.5e-5 ref_p = 1.01325 gen_vel = yes gen_temp = 298 gen_seed = 173529 constraints = all-bonds constraint-algorithm = Lincs lincs-order = 4 lincs-iter = 1 The first box was a cube with the side length 8.6 nM and comprises 9 types of molecules with these MW and number: NUMBER MW Charge Diff A 10 229.26 NEG 0.2262 Meth 7736 46.09 0.4248 Na 29 22.98976 POS 0.0116 H2O 310 18.01528 0.0339 B 9 233.2893 0.007 C 9 234.29724 NEG 0.0041 D 10 587.82778 POS 0.0037 E 10 586.81984 POS-NEG 0.0063 I 20 126.90447 NEG 0.0048 The second box was a cube with the side length of 4.11 nM and comprises the same molecules but with a considerable reduction in concentration of water and methanol: NUMBER MW Charge Diff A 10 229.26 NEG 0.7074 Meth 1130 46.09 0.9537 Na 29 22.98976 POS 0.1017 H2O 230 18.01528 0.1909 B 9 233.2893 0.014 C 9 234.29724 NEG 0.0167 D 10 587.82778 POS 0.0104 E 10 586.81984 POS-NEG 0.0107 I 20 126.90447 NEG 0.0107 Hence, the diffusion coefficient in the smallest box is higher than in the bigger box. Is this result normal? Thnx in advance, Riccardo -- 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.