ProtoMol v2.0/v3.0

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.

ProtoMol v2.0 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 v3.0 simulations can be visualized using the Open Source Jave Molecular Viewer, included in the download package.

ProtoMol is freely distributed software, and the source code is available.

Key Features of ProtoMol 3.0

Key Features of ProtoMol

Structural BioCore/Biology Software Database: ProtoMol.