Software

Molecular Dynamics is an approach to physics based simulation.

Protomol

Open source 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. ProtoMol has been designed to interact with JMV, our Java molecular viewer, that is used for displaying large biomolecular systems in three dimensions.

Protomol embodies the new NML method in addition to standard MD methods. We have now issued version 3 as part of our Folding@Home project, in conjunction with the Pande group at Stanford University.

New features available in Protomol 3:

• Normal Mode Langevin method
• OpenMM GPGPU integration
• GROMACS/Amber force field in addition to CHARMM
• Folding at Home core
• Java OpenGL viewer integration
• Langevin Leapfrog method
• Fast Hessian diagonalization
• Generalized Born implicit solvent
• SCPISM implicit solvent

Hard sphere simulation.

Thanks for reading!