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:
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Used the CHARMM36 force field
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Ran 200 ns simulation (MD run)
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20 ns NVT
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100 ns NPT
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Then added the organic molecule and ran another 100 ns
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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:
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Separately for each system (pure water, pure DES, organic in water, mixture),
or
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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!