Using GROMACS and PLUMED to do a metadynamics simulations

User discussions
1

GROMACS version: module load GROMACS/2024.4-foss-2023b-CUDA-12.4.0-PLUMED-2.9.2
GROMACS modification: No

Hi everyone

I’m trying to perform a metadynamics simulation with plumed and compare the differences in the protein between the apo structure (protein alone) and the holo structure (protein + ligand). But I’m not sure if the procedure that I’m doing is correct or not…Can someone help me with this?

2

This is not GROMACS question, rather than methodological approch you need to decide. May be check out the literature for the similar works/system.