Protomol Software Infrastructure

PROTOMOL is a program for molecular dynamics (MD) simulations using non-bonded, bonded, short-range, and long-range forces optimized for tens of thousands of atoms representing water and several large molecules. It evolved from SAMD 2 [155], a prototyping program for MD that uses templates and inlining to achieve high performance C++ code. SAMD 2 was slightly faster than NAMD 2.1 on a test of solvated BPTI with 15000 atoms. To the best of our knowledge, NAMD 2.1 is the fastest MD program available [].

The design of the PROTOMOL infrastructure is shown in Fig. 1. PROTOMOL shares the goals of high performance, maintainability, and generic modules. For example, there is a generalized MTS integrator hierarchy, support for arbitrary pairwise force fields, periodic boundary conditions of any shape, system and extended system Hamiltonian, and grid hierarchies.

  
Figure 1: PROTOMOL collaboratory infrastructure.