# Viscosity calculation for protein cluster

**URL:** <https://gromacs.bioexcel.eu/t/viscosity-calculation-for-protein-cluster/5510>\
**Category:** User discussions\
**Created:** [December 30, 2022, 7:45pm UTC](https://gromacs.bioexcel.eu/t/viscosity-calculation-for-protein-cluster/5510 "2022-12-30T19:45:43Z")\
**Posts on this page:** 1\
**Page:** 1

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**Author:** ![Sanchari](https://avatars.discourse-cdn.com/v4/letter/s/9fc29f/32.png) [@Sanchari](https://gromacs.bioexcel.eu/u/Sanchari)\
**Post date:** [December 30, 2022, 7:45pm UTC](https://gromacs.bioexcel.eu/t/viscosity-calculation-for-protein-cluster/5510/1 "2022-12-30T19:45:43Z")

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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.