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.