Protein small molecule simulation

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1

GROMACS version:2020.6
GROMACS modification: Yes/No
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I want to simulate an IDP protein with a small molecule. I want to add 10 copies of the same molecule into the simulation box randomly and look for its interactions with the protein molecule then what should be a suitable approach to prepare the system? Can anyone suggest?

2

Gromacs has the insert-molecule function which should work for randomly inserting molecules (check out Building Biphasic Systems for an example of how it’s used and gmx insert-molecules - GROMACS 2026.2 documentation for more precise documentation)