The GROMOS Biomolecular Simulation Program Package

TLDR

GROMOS96 is a biomolecular simulation package that uses molecular dynamics, stochastic dynamics, energy minimization, and path‑integral methods to model biomolecules. The authors introduce GROMOS96 and illustrate its new capabilities through two applications: local elevation simulation and four‑dimensional molecular dynamics. GROMOS96 expands on GROMOS87 by adding new methodologies, organizing a 73,000‑line FORTRAN77 codebase with emphasis on reliability, testing, and efficiency, and demonstrating these features in the two applications.

Abstract

We present the newest version of the GROningen MOlecular Simulation program package, GROMOS96. GROMOS96 has been developed for the dynamic modelling of (bio)molecules using the methods of molecular dynamics, stochastic dynamics, and energy minimization as well as the path-integral formalism. An overview of its functionality is given, highlighting methodology not present in the last major release, GROMOS87. The organization of the code is outlined, and reliability, testing, and efficiency issues involved in the design of this large (73 000 lines of FORTRAN77 code) and complex package are discussed. Finally, we present two applications illustrating new functionality: local elevation simulation and molecular dynamics in four spatial dimensions.