Dissemination of methods and software

All the methods described here are implemented in a program developed in our group called PROTOMOL It is a parallel, object-oriented, component-based framework for MD simulations [50,48,65]. The framework is designed for non-bonded, bonded, short-range and long-range forces for applications with tens of thousands of atoms representing biomolecules and solvents. It has a modular design that allows for easy prototyping of complex methods. PROTOMOL has been released and is available through http://www.nd.edu/~lcls/Protomol.html.

There are excellent MD programs such as AMBER [95], CHARMM [12], NAMD [53], SPASM [8], X-PLOR [16], PINY_MD [92], and many others [7,15,23,42,64,81]. Indeed, one has to answer the question, why another MD program? Our answer is that many design decisions of programs intended for production simulations render them inappropriate to serve as an algorithm-development and academic-research platform.

It supports MTS integrators including various MOLLY methods and Verlet-I/r-RESPA, the CHARMM 19 and 28 force field [63,62], and Ewald [19,29,30,32,37,55,58,70,80,86,85] and Particle Mesh Ewald [25] fast electrostatics. This makes it a flexible platform for algorithmic development. It also supports interactive MD [87] through a connection to the program VMD of the University of Illinois [41]. These capabilities were demonstrated with a haptic device in a research booth at Supercomputing 2000. PROTOMOL runs on UNIX platforms and efforts are underway to port it to Windows and Macintosh OS X. This program is currently used by our collaborators in the United States and in Norway, but with our recent release it will be more widely available.