Calculating Diffusion Coefficient of benzene using MDAnalysis

User discussions
1

I am calculating the diffusion coeffiicient of a benzene molecule in water using MDAnalysis, but when I calculate the value of each individual carbon or hydrogen atom, they differ significantly.

Is there a way to calculate the diffusion coefficient of the molecule as a whole (perhaps by using the center of mass) and if so, how would I do this?

2

You can select the whole benzene residues,something like this after reading the topology:

benzene = u.select_atoms('resname XXX')

anyway, it would be better to ask in MDanalyis forum.