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?
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)
How to calculate how many molecules are interacting with the protein in each frame of the entire simulation trajectory and those that are interacting how long do they interact?
Depends a bit on what you mean by interact. One option would be to create a contact map based on the minimum distance between molecules and protein (you can extract distances using mindist gmx mindist - GROMACS 2026.2 documentation , or gmx distance or pairdist, depending on what you’re trying to achieve). You could also count hydrogen bonds (How to study Hydrogen bonds using GROMACS - Compchems) or look at electrostatic interactions (see Protein-Ligand Interaction Energy in Protein-Ligand Complex ). In terms of counting the number in each frame and for how many frames, I don’t think there’s a specific gromacs function built in, you may just have to define the necessary index groups with gmx make_ndx, output the contacts you defined, then write up a script to count based on what you’re looking for