Shear viscosity calculation

GROMACS version:2024.1
GROMACS modification: Yes/No
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Is there any smaple mdp file to calculate shear viscosity of drug molecule in water? I already obtained diffusion coefficient of drug molecule in water. Do the files obtained during msd run work for calculating viscosity? I will be much thankful if any one could help me to know the steps to be followed to calculate shear viscosity.

Hi,

I am not sure if it makes much sense to calculate the viscosity of ‘a molecule’. Do you mean the viscosity of an acqueous solution of drug molecules?

You can use gmx energy -evisco to calculate the viscosity coefficient using Einstein’s formula. Otherwise you can look into cos-acceleration or deform (.mdp options), which also offer a way to compute viscosity.

@MichelePellegrino
yes i want to calculate viscosity of a drug equilibrated in water I have calculated diffusion using equilibration md but I think to calculate viscosity I need non eq md but I cant find any reliable mdp file to get reference how should I handle it can you suggest me any mdp file what should be it like

There is no such thing as “the viscosity of a molecule in water”. Why do you want to compute this?

One could compute the viscosity of a certain concentration of drug molecules solvated in water. If this concentration is low, the viscosity will be very close to that of pure water.