ProtoMol A framework for molecular dynamics simulations.
Download

ProtoMol Ranking & Summary

ProtoMol Tags

simulation simulate simulator molecular damping dynamics Molecular View Molecular Dynamics Package molecular interaction networks molecular visualization molecular editor Molecular Mining molecular dynamics simulation bio-informatic framework DCD trajectory file simulate molecular dynamics molecular diameter Molecular Simulation Molecular System find molecular substructure Molecular Dynamics animate molecular trajectory molecular dynamics analyzer molecular phylogeny study molecular dynamics molecular phylogenetics simulations software simulations

ProtoMol Description

ProtoMol is a useful object-oriented, component based, framework specially designed 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. Main features: An object-oriented component based framework for molecular dynamics simulations Designed for high flexibility, easy extendibility and maintenance, and high performance demands Incremental parallelization combining sequential and parallel environment Support of generic multiple time-stepping integration schemes Generic forces and potentials Fast electrostatic force evaluation algorithms: Ewald summation, O(N3/2) Particle-Mesh-Ewald, O(N log N) Multi-grid method, O(N) Support of common I/O formats (pre- & post-processing) 106 particle systems

ProtoMol Related Software