From: Axel Kohlmeyer (
Date: Thu Oct 22 2020 - 13:47:24 CDT

two comments:

1) RMSD != sqrt(MSD) those are completely different entities.

2) you can use the pbctools plugin to unwrap a wrapped trajectory.


On Thu, Oct 22, 2020 at 2:33 PM RonitS Chem <> wrote:

> Hello all,
> I want to calculate the diffusion constant for a number of water models
> and so need to calculate the MSD from the 2ns trajectories I have. I am
> using my own python code, but I realize that since the periodic boundary
> condition is under effect I cannot calculate the distances properly.
> Since I use VMD to print out the snapshots for MSD calculations, is there
> any way to account for PBC? I would like to get rid of it, in other words
> get the unfolded coordinates for the atoms but I do not know how to do it.
> Any help or insight would be much appreciated.
> I have seen the RMSD tool in VMD but when I calculate the RMSD and square
> it to get the MSD, it is not a straight line as expected. I assume this is
> because of the PBC as well. I am fairly new to all this, so please forgive
> me if I am missing something simple.
> Sincerely,
> Ronit

Dr. Axel Kohlmeyer
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.