[gmx-users] Diffusion constant

[pari lotfi]

Dear all,

I saw in the different simulation that the number of restart point affect
on the D! What is the rule of restart point on the diffusion constant
calculation?

*"The diffusion constant is calculated by least squares fitting a straight
line"*

Then all the "msd" doesn't rule in fitting and D?

If yes, how do I select least squares?


*"note that t is time from the reference positions, not simulation time" *
What is reference position? Are the reference point and restart point is
the same? How can I fit on references position instead simulation time?

Thanks,
Pari