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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