[gmx-users] Self Diffusion contant

It is an interesting question. Is it not worthwhile to have a separate forum board for such methodological issues? Some time ago I raised the similar question regarding the convergence of Self Diffusion Coefficient. The reasoning given in the paper mentioned by Javier seems to be related to my i

Re: [gmx-users] Self Diffusion contant

This is the normal behaviour for a MSD vs. time plot. Actually, as set by default in g_msd, neither the first seconds nor the last ones are taking into consideration to calculate the difussion constant. The explanation for the non-liear curves might be the following. On one hand, at the begini

[gmx-users] Self Diffusion contant

Dear Gromacs, I have been calculating the self Diffusion constant of my system. Surfactants in a different solvents of the same volume. After simulation for 20ns I found the following data for the trajectory of the mean square displacement. # D[ TPA] = 0.2039 (+/- 0.0503) (1e-5 cm^2