# Help me in Viscosity Calculation using Growmacs

**URL:** <https://gromacs.bioexcel.eu/t/help-me-in-viscosity-calculation-using-growmacs/13359>\
**Category:** User discussions\
**Created:** [April 4, 2026, 12:40pm UTC](https://gromacs.bioexcel.eu/t/help-me-in-viscosity-calculation-using-growmacs/13359 "2026-04-04T12:40:29Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![Debabrata99](https://avatars.discourse-cdn.com/v4/letter/d/e99b99/32.png) [@Debabrata99](https://gromacs.bioexcel.eu/u/Debabrata99)\
**Post date:** [April 4, 2026, 12:40pm UTC](https://gromacs.bioexcel.eu/t/help-me-in-viscosity-calculation-using-growmacs/13359/1 "2026-04-04T12:40:29Z")

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Hello everyone,

I hope you’re all doing well. I’m currently working on a GROMACS MD project where I’m trying to calculate viscosity and understand how an organic molecule is extracted from water using a deep eutectic solvent (DES). I’ve read a few recent papers, and it seems like the Green–Kubo method and shear viscosity are good approaches, but I’m still a bit confused about how to proceed properly.

So far, here’s what I’ve done:

- Used the CHARMM36 force field

- Ran 200 ns simulation (MD run)

- 20 ns NVT

- 100 ns NPT

- Then added the organic molecule and ran another 100 ns

- The system looks stable and even shows a nice layering in the trajectory.

My general workflow has been:

Energy minimization → NVT → NPT → Production MD

**I have a few questions and would really appreciate your suggestions:**

1. What should I do next for viscosity calculation?

2. Which system should I focus on?

Is it better to calculate viscosity:

- Separately for each system (pure water, pure DES, organic in water, mixture),

- Only for the final mixture where extraction actually happens?

3. .mdp settings confusion, do I need to change the .mdp files and run the file again ?

4. What should my workflow be now?

If anyone has worked on similar systems (DES, viscosity, or extraction studies), I’d really appreciate your guidance. Even small suggestions would help a lot.

Thanks in advance!

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<div class="post-metadata">

**Author:** ![hess](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/hess/32/416_2.png) [@hess](https://gromacs.bioexcel.eu/u/hess)\
**Post date:** [April 8, 2026, 7:06am UTC](https://gromacs.bioexcel.eu/t/help-me-in-viscosity-calculation-using-growmacs/13359/2 "2026-04-08T07:06:40Z")

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It seems like you do not have a clear picture of your scientific questions. You should get those clear before.

For viscosity calculations you can use Green-Kubo/Einstein, with gmx energy, with an equilibrium simulation or a non-equilibrium simulation using shear flow with the deform option. Both are described in the manual.