GROMACS modification: Yes/No
Here post your question
My two peptides are situated at 4 nm apart from each other. I want to calculate interaction energy along com distance between two peptides from 0 to 4 nm com distance.
if you want to calculate the potential of mean force between two peptides you can use the pull code (Non-equilibrium pulling — GROMACS 2021.4 documentation) and the peptides’ com distance as reaction coordinates.
For mdp parameter looks here (Molecular dynamics parameters (.mdp options) — GROMACS 2021.4 documentation)
for an example look here Umbrella sampling — GROMACS tutorials https://tutorials.gromacs.org documentation