[gmx-users] Diffusion coefficient water

[Diez Fernandez, Amanda]

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