GROMACS version:
GROMACS modification: Yes/No
Here post your question
I have performa 500 ps simulation of just the water molecules (SPC) model. Towards the end I can see a curve. I am unable to understand the reason behind it. can anyone explain ?
I would say that 100 water molecules and 500ps are both a very limited number of molecules and a very short time. You should have a longer run with many more molecules, as I can’t even think about how can 100 molecules fit in a box without PBC artifacts.
there were around 8000 water molecules in the box but i wanted to check the MSD of a few 100.
Why? Does the kind stay there if you do the average over all the water molecules?
no, its a linear line when I average over all water molecules.
Then probably you have your answer: you need more statistics to get a better MSD estimate! :)
I might be wrong, but also I think the associated error to your diffusivity from the MSD you plot is going to be small even with the kind. Nevertheless, the more statistics the better.
The MSD curves tend to be noisier as time increases since the variance in molecule displacement becomes higher (there is more time for molecule pathways to diverge in the chaotic system), so that’s why you get the noise at the end of the curve. As previously discussed in this post, including more water molecules in your average should get rid of the bump.
Hope this answered your question!
Thank you so much
Thank you so much. I can better understand it now
