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

• Interface to OpenMM, an MD library with NVIDIA and ATI general purpose GPU support. OpenMM supports AMBER force fields and Generalized-Born implicit solvent.

• Python bindings offered as MDLab, which allow for prototyping of high level sampling protocols, new integrators, and new force calculations in Python.

• Coarse grained normal mode analysis (CNMA), which provides a scalable O(N^9/5) time and O(N^3/2) memory diagonalization. CNMA approximates low frequency modes very well.

• Normal Mode Langevin (NML) dynamics, which uses CNMA to periodically compute low frequency bases for propagation of dynamics, while fast modes are minimized to their equilibrium position. NML allows timesteps of 100 fs and more for even small proteins (> 30 residues) with real speedups that are about a third of the timestep used.

• Full checkpointing support, which simplifies use in distributed computing platforms such as Condor or Folding@Home.

Key Features of ProtoMol

• 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(N^3/2)
  • Particle-Mesh-Ewald, O(N log N)
  • Multi-grid method, O(N)
• Support of common I/O formats (pre- & post-processing)
• 10⁶ particle systems

• Supported platforms:
  • Sun/Solaris
  • AIX (optional with MPI)
  • HP-UX (optional with MPI)
  • IRIX (optional with MPI)
  • Linux (optional with MPIch or LAMMPI)
  • Windows

Structural BioCore/Biology Software Database: ProtoMol.