ProtoMol is an object-oriented, component based, framework for molecular
dynamics (MD) simulations. The framework supports the CHARMM 19 and 28a2 force
fields and is able to process PDB, PSF, XYZ and DCD trajectory files. It is
designed for high flexibility, easy extendibility and maintenance, and high
performance demands, including parallelization. The technique of multiple
time-stepping is used to improve long-term efficiency. The use of fast
electrostatic force evaluation algorithms like Ewald, particle Mesh Ewald (PME),
and Multigrid (MG) summation further enhances performance. Longer time steps
are possible using MOLLY, Langevin Molly and Hybrid Monte Carlo, Nose-Hoover,
and Langevin integrators. In addition, ProtoMol has been designed to interact
with VMD, a visualization engine developed by the University of Illinois that is
used for displaying large biomolecular systems in three dimensions. ProtoMol is
freely distributed software, and the source code is available.