Distances during the simulation

User discussions
1

GROMACS version:2020.3
GROMACS modification: No

Hello Gromacs users!

I was running protein-ligand simulation and would like to know if I can use gromacs tools to get an output of all atoms that during the simulation got closer than 4A to a specific ligand atom + distances

Regards,
Gil

2

Hi,
the tool gmx mindist can be what you are looking for. With the option -d you can define the distance for contact.
see gmx mindist — GROMACS 2020.5 documentation
Best regards
Alessandra