GROMACS version:2020.3

GROMACS modification: No

I would like to compute the diffusivity of methanol in a zeolite using the gmx msd command, but I am confused about the concept of “reference points”

In the first paragraph of the description of the command (http://manual.gromacs.org/documentation/current/onlinehelp/gmx-msd.html#gmx-msd), it says: "

The time between the reference points for the MSD calculation is set with

`-trestart`

."

**What are these “reference points”?**

Furthermore, it says:

The diffusion constant is calculated by least squares fitting a straight line (D*t + c) through the MSD(t) from

`-beginfit`

to`-endfit`

(note that t is time from the reference positions, not simulation time)

Before I read this, I thought that t was the simulation time, but clearly it is not. However, I don’t understand what it is because I don’t get the concept of “reference points/positions” :(

In the penultimate paragraph of the Description section, it says:

The diffusion coefficient is determined by linear regression of the MSD, where, unlike for the normal output of D, the times are weighted according to the number of reference points, i.e. short times have a higher weight.

I am not able to understand this sentence, because I don’t get the concept of “reference points”

Furthermore, it says that the “diffusion coefficient” is different from “the normal output of D”.

What is “normal output of D”? Where can I find it?

Thanks for your help.

I think that once I understand the concept of “reference points”, I will be able to make some progress.