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:

Folding at Home.

We now have a Folding at Home (F@H) workserver hosted by the Center for Research Computing, connected to the F@Hservers at Stanford University. This allows us access the F@H supercomputer for our simulations. As of 22nd February we have access to over 120,000 nodes. F@H is famous for achieved a computing power of 1 petaflop, or 1 quadrillion floating point operations per second, for which it received a Guinness Book of records award.


Graph courtesy of the Pande group at Stanford University.