Here is a list of open-source software I have developed (by my own or in collaboration with other people) that could be useful to other researchers:
oxDNA: is a molecular simulation code that is mostly used to run simulations of the oxDNA/oxRNA coarse-grained models, although it supports many other models. It can run on single CPU cores or single GPUs. More details can be found here.
cogli2 is a a simple tool to visualise configurations of coarse-grained simulations. It is straightforward to use and it is designed to facilitate the making of publication-ready figures.
PatchyParticles is a code for perfoming Monte Carlo simulations of hard particles decorated with four patches modelled through the Kern-Frenkel pair interaction potential. It was originally developed to accompany a review paper.
tacoxDNA is a collection of tools to generate oxDNA configurations starting from other formats, as described here.
pyrla is a Python script that launches parallel processes executing different commands. Its most common use case is to build a hierarchy of directories (e.g.
Temperature_T/Pressure_P, for several values ofPandT), and then launch a (possibly different) command in each one.baggianalysis is a library aimed at simplifying the analysis of particle-based simulations. It makes it easy to parse, convert and analyse trajectories generated by simulation codes in an agnostic way. It is written in C++ and comes with Python bindings.