GROMACS version: 2025
GROMACS modification: Unsure
Hi. I am new to GROMACS and have zero knowledge on coding. I want to stimulate a protein that has its signal peptide attached to the N-terminus of the protein and to molecular simulate how the mutation affect the conformation of the signal peptide with respect to its interaction with lipid bilayer. It would be great if someone can provide the most fundamental tutorial to this so that I can get started.
Thank you.
A couple of very relevant suits of tutorial are this and this. If you are new, I highly suggest you these three from the suits I linked
- Tutorial 1: Lysozyme in Water
- Introduction to Molecular Dynamics
- Introduction to Membrane-Protein Simulation
This will guide you in the basics of MD workflow and protein/membrane simulations.
Most importantly, try to define very well your problem and what you want to simulate. Once you have some basic concepts, look in literature and see if anyone tried to do what you want to do. Did they succeed? Fail? Why? And build from there.