Below some programs and tools/scripts I wrote are listed, each with a short description and a link. Some of them are on github, with some documentation and examples, while the rest can be downloaded from this web page. Feel free to contact me with questions or comments.

On Github

icemas Molecular Dynamics in C++
fogal Implementation of a genetic algorithm for the optimization of force field parameters
based on DFT energies and forces
fomc Monte Carlo implementation for the optimization of Lennard Jones parameters in molecular force fields
gmxstrain Script to calculate finite temperature elastic constants and moduli for organic molecular crystals
based on MD trajectories
aspbe A fast solver for population balance equations, that can be used to model the impact
of process parameter settings on the results of anti-solvent crystallization.
Can be used as part of PAT equipment to control the progress of protein crystallization.

Direct download

openmm-protein-ligand-complex-mmgbsa-sa A python script using openmm to optimize a protein-ligand complex via simulated annealing
gcsf Grand canonical MC/MD for LJ fluids, written in C
gmx-ffoplsp Extension of the FFOPLS-aa FF for synthetic organic polymers, in Gromacs rtp format
mkr0 Generation of initial structures/solvation for MD simulation, C++
delfrag Deletion of a fragment from a series of molecules
C++, compile with gcc, requires libopenbabel
symchg2 Symmetrizes partial charges on input molecules
Python, requires the Openeye OEChem library.
dips Distance between a point and an atom defined by a smarts fragment
C++, compile with gcc, requires libopenbabel