GROMACS version:5.1.5
GROMACS modification: Yes/No
I am trying to calculate viscosity of a cluster of proteins in solution. I have set up the system using MARTINI 2.2 force field. I was following the gmx energy -vis method, however, I am not quite sure whether it gives shear viscosity specifically for the protein end-to-end distances. How do I calculate the autocorrelation time of the end-to-end protein distance and average over all the proteins? I will be thankful if anyone could help me with the steps needed to calculate shear viscosity.