Is there a way to pull ligand into the protein binding site?

[seke]

GROMACS version: 2018
GROMACS modification: No

I have seen works on pulling of ligand into GPCR using Supervised MD. Is there a way to implement such simulations in Gromacs? Something like a ‘reverse’ pulling ( commonly used in umbrella sampling).

[alevilla]

Hi,
I am not familiar with Supervised MD. But you can perform umbrella sampling using GROMACS. See for details on the

Non-equilibrium pulling — GROMACS 2020.4 documentation

Molecular dynamics parameters (.mdp options) — GROMACS 2020.4 documentation

Best regards
Alessandra