GROMACS version: 2018.4

GROMACS modification: No

For my bulk simulation of compound, the diffusion constant (D) came out to be 0.4069 (+/- 0.0303) 1e-5 cm^2/s from gmx msd command, the gmx msd discription says it calculates D by fitting a line to msd vs time plot, but when I fitted a line to msd vs time data, I get slope = 0.002462 and intercept of 0.204, the slope value is not matching with the D value given by gmx msd, am I missing something here? Is there some constant we need to multiply at the end to get answer in cm^2/s units. Please help. Thank you.

Hi,

`gmx msd`

by default fits the center range 10%–90% along your time axis, making the assumption that the slope is linear there (which one should confirm).

Is your fit using that same range?

Regards,

Petter

Even if I do so, by looking at the data points it seems to me, it will not make much of a difference, the data is almost linear, slope will not change much from 0.002. Still I fitted data for 10%-90% data, I got new slope of 0.00244.

Ahh, I got it.

*msd = 6D + intercept*

So, slope is equal to 6 multiplied by diffusion constant, also default msd units are nm2/ps, hence when we change it to cm2/s, we need to multiply by 0.01, so we get gromacs given value:

D = 0.002462*0.01/6 = 0.4