| [GROMACS](http://www.gromacs.org) | GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. |
| [PLUMED](http://www.plumed-code.org) | PLUMED is an open source library for free energy calculations in molecular systems which works together with some of the most popular molecular dynamics engines. Free energy calculations can be performed as a function of many order parameters with a particular focus on biological problems, using state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. The software, written in C++, can be easily interfaced with both fortran and C/C++ codes. |
| [RELION](http://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page) | RELION (for REgularised LIkelihood OptimisatioN, pronounce rely-on) is a stand-alone computer program that employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class averages in electron cryo-microscopy (cryo-EM). |
## Cae
| Module | Description |
| ------ | ----------- |
| COMSOL | |
| [deMonNano](http://www.demon-software.com) | deMonNano is a software package for density functional theory based tight binding calculations. It is part of the deMon (density of Montréal) suite of programs. The present version of the code of deMon for DFT is now known as deMon2k. This code and general information about deMon are available at http://www.demon-software.com |
| OpenFOAM | |
## Chem
| Module | Description |
| ------ | ----------- |
| ABINIT | |
| [ASE](https://wiki.fysik.dtu.dk/ase/) | ASE is a python package providing an open source Atomic Simulation Environment in the Python scripting language. |
