[gmx-users] abnormal MSD values
Riccardo Concu
ric.concu at gmail.com
Thu May 15 11:09:42 CEST 2014
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
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