Hi All,
I calculated the MSD using the gmx msd -f run05.part0005.xtc -s run05.tpr -o msd_240-250ns.xvg. As a result, I got a graph with 2 slopes as attached. Does this imply that there are two types of diffusion in the system? I appreciate your help.
Thank you very much.
It can, but that isn’t conclusive. It would help to watch the trajectory to see if that can indeed be the case, as it might very well also be e.g. a PBC artifact. Did you use the -nojump option of gmx trjconv in processing the trajectory? If not, please try and see if this behavior persists.
Thank you very much for your comment. Yes, even with -pbc nojump option in gmx trjconv, the behavior of the graph is the same.
I see you’re also using only part 5 of the simulation - I would definitely check if that behavior is replicable and does not depend on e.g. a single binding/unbinding event before coming to any conclusions.
Hi,
I followed a simulated annealing schedule for every 25 ns. Since I get the kink at 25 ns, I believe this behavior is due to the annealing schedule. I want to calculate the diffusion coefficient of water in the system. With this behavior of my MSD graph, now I am confused about how I get the diffusion coefficient of water. Appreciate your help.
Thanks
