[gmx-users] Diffusion coefficient water

[li he]

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.diez10 at 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
> --
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