ProtoMol v2.0 Release

31 May 2005

We are pleased to announce the release of ProtoMol v2.0: a free, open source, object-oriented, component-based framework for molecular dynamics (MD) simulations. It supports CHARMM 19 and 28a2 force fields and is able to read and write PDB, PSF, XYZ, DCD, and several common graphics formats. ProtoMol is designed for high flexibility, ease of extendibility and maintenance, and high performance and scalability demands. We use MPI to implement atom- and force-based decompositions in a manner nearly transparent to both end-users and developers. The use of fast electrostatic force evaluation algorithms like particle mesh Ewald (PME), an O(n log n) method, and multigrid summation (MG), an O(n) method, further improve performance. In addition, MG has superior scalability when running in a parallel environment.

ProtoMol contains many novel MD and Monte Carlo (MC) based methods suitable for simulation in a variety of ensembles. For example, shadow hybrid Monte Carlo (SHMC) has been shown to scale with system size and MD timestep by a factor of 10 or more over hybrid Monte Carlo (HMC). Multiscale simulations take advantage of longer timesteps by coupling multiple time-stepping algorithms with advanced integrators. Using targeted Molly, we have achieved stable timesteps of 16fs for solvated proteins. In addition, ProtoMol has been designed to interact with VMD, a visualization engine developed at the University of Illinois, which is used for displaying large biomolecular systems and running simulations in 3-D.

Highlights of ProtoMol v2.0:

We invite you to visit the ProtoMol home page,, where C++ source code, documentation, and prebuilt binaries may be found. Operating systems natively supported include Linux, SunOS, Irix, HP-UX and Windows.

We have also configured a new mailing list to better serve our user base. Please visit the following link and join the list for support and development news:

Protomol user and development questions can be sent to the list using the following email address:

For questions or comments, please feel free to contact the ProtoMol team at .