[gmx-users] Regarding correct way to calculate diffusion constant

Apramita Chand apramita.chand at gmail.com
Fri Aug 26 15:26:15 CEST 2016

Dear All,
I want to calculate the diffusion constant of urea in my system. I used
g_msd  for this purpose and the value came to be 8.279e -08 (+/-8.85e-09)
1e -5 cm^2/s. Since the value is quite low, I wanted it to check it with
result from VACF.
 So I used the commands:
g_velacc -acflen 1001 -no normalize -mol -n index.ndx -s md.tpr -o
g_analyze -f vac_urea.xvg -integrate

The result comes to be
Read 1 sets of 1001 points, dt = 1

Calculating the integral using the trapezium rule
Integral 1     0.05625  +/-    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   1.177023e-04   3.907055e-03   1.235519e-04      19.658   328.889

 Is the integral value 0.05625 or 1.177023e-04? In the gromacs manual, it
says to multiply by 10^-6 and divide by 3 while in the forum it was
suggested that it should be multiplied by a 333.33.
How should the diffusion constant be correctly calculated?
Any explanations as to why g_msd yielded a low value for a system
conatining 5 urea,751 water and a single protein molecule?

Thanking you,
yours sincerely,
Apramita Chand

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