1.- Molecular Dynamics simulations of DNA in LAMMPS
In this link you will find a gitlab repository with detailed instructions on how to perform Molecular Dynamics simulations of DNA using models at different level of resolution: bead-spring, double-stranded DNA and oxDNA. The material was originally prepared as part of the EUTOPIA summer school in Paris (July 2022). Since then, I have improved certain aspects with the feedback from users. For instance, you can find the codes to compute the Twist, Writhe and Linking number of a ribbon and also, the elastic constants for the oxDNA1 and oxDNA2 models.
2.- Landau Mean Field theory
In this Link you will find a gitlab repository with Mathematica notebooks to generate interactive plots of the Free Energy Landscape and compute its minima, for different classical systems (Ising model, Flory-Huggins model).
3.- All atom simulations of linear-DNA with GROMACS
In preparation…
4.- Metadynamics simulations with the oxDNA model
In preparation…