Repository of the different codes developed during my M2 insternship at the ILM.
Inside the water/ directory. Run eau_CLI -h for manual of the CLI The bash files are automated pipeline for single run, analysis of the cutoff and of the simulation length of water MD simulations.
File for automated running gromacs. Energy minimization, equilibration NVT/NPT, production, analysis.
File for submiting jobs to the PSMN on the correct node.
✉️ Mercure is a submit script to break down in smaller simulation one big simulation. See documentation in PSMN/Mercure
Test outputs of the various script done.
Various codes that use MSM or PyEmma
🚅 Lethe is an implementation of automatize PyEmma MSM pipeline. Manual available using ./LETHE.py -h/--help or in Markov/Lethe
Codes that rely on TTClust and extract its result
Scripts for VMD