GROMACS version: 2024.5 & 2021.5
GROMACS modification: No
Hi. I am currently calculating the MSD and diffusion coefficient (D) of a molecule called mytomicin (MMC). I have a system where I place 3 MMCs in a water solution using SPC water model. I have run 5 different 20ns long MD production runs in NPT ensemble, varying the frecuency at which each frame of the md.xtc is recorded: 1 frame per 1000, 100, 10, 2, 1 ps. These 5 runs have been carried out in both Gromacs 2024.5 and Gromacs 2021.5 (10 runs in total)
As these images shows, the MSD can vary a lot from one recording frecuency to another, and in most cases curves dont ressemble a tendency. Does this mean that the recording frecuency is affecting the calculation of the MSD? I cannot understand how it is possible…
And I have done the msd calculation with the gmx msd command in Gromacs 2024.5 and Gromacs 2021.5 versions. Here you have the MSD calculation for water. Does it have any explanation?
