[gmx-users] Comparison of diffusion constant from Einstein and Green Kubo
abhishek khetan
askhetan at gmail.com
Mon May 2 14:51:48 CEST 2016
Dear gmx-users,
I wanted to calculate the diffusion coefficient of lithium ions is a
solution. I tried using the gmx msd routine first with the options -nomw
and -mol. I want to know if -nomw should be used or not if I want to
compare my results with experiments. Anyway The result I obtained from here
was :
$ gmx_mpi msd -f dms216_16lino3_npt.xtc -s npt.tpr -n index.ndx -o li.xvg
Fitting from 100 to 900 ps
D[ LI] 0.1093 (+/- 0.0086) 1e-5 cm^2/s
Next, i tried using the velacc routine as:
gmx_mpi velacc -f dms216_16lino3_npt.trr -s npt.tpr -n index.ndx -o li.xvg
and then integrated it using the analyze routine to get the result
$ gmx_mpi analyze -f li.xvg -integrate
Read 1 sets of 101 points, dt = 5
Calculating the integral using the trapezium rule
Integral 1 2.36293 +/- 0.00000
std. dev. relative deviation of
standard --------- cumulants from those of
set average deviation sqrt(n-1) a Gaussian distribition
cum. 3 cum. 4
SS1 9.644851e-03 9.989920e-02 9.989920e-03 6.042 30.877
When I multiply the obtained result ( 2.36293) by 10^(-2) and divide by 3
to get the final answer in cm2/s, the value is 7.87 x 1e-3 . This is orders
of magnitude different from the einstein style calculated D = 0.1093 (+/-
0.0086) 1e-5 cm^2/s. I tried increasing the -dt value to 100 and then the
output I get is:
Read 1 sets of 6 points, dt = 100
Calculating the integral using the trapezium rule
Integral 1 64.40000 +/- 0.00000
std. dev. relative deviation of
standard --------- cumulants from those of
set average deviation sqrt(n-1) a Gaussian distribition
cum. 3 cum. 4
SS1 1.990000e-01 3.611937e-01 1.615307e-01 1.079 0.362
Which is much worse off. Can anyone please suggest what I might be doing
wrong.
Best,
--
MfG,
abhishek
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