Calculation of distance between two atoms (amino acid and linad)

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1

GROMACS version: 2022
GROMACS modification: Yes/No
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How can I calculate distnace between two atoms (interacted amino acid and lignad molecule’s atom).
How will I select a particular atom of amino acid and ligand which are interacting.

Please help me.

2

gmx distance -h might be a good start.

3

Thank you for your suggetions

How can I make index file of a particular atoms of proteins amino acid and nearest atom of lignads with that amino acid

4

If the selection changes during the trajectory it is not very easy. Otherwise you could follow the instructions of gmx distance, especially the -select option.