Parallel molecular dynamics simulations of biomolecular systems

Abstract

We describe a general purpose parallel molecular dynamics code, for simulations of arbitrary mixtures of flexible molecules in solution. The program allows us to simulate molecular systems described by standard force fields like AMBER, GROMOS or CHARMM, containing terms for short-range interactions of the Lennard-Jones type, electrostatic interactions, covalent bonds, covalent angles and torsional angles and a few other optional terms. The state-of-the-art molecular dynamics techniques are implemented: constant-temperature and constant-pressure simulations, optimized Ewald method for treatment of electrostatic forces, double time step algorithm for separate integration of fast and slow motions. The program is written in standard Fortran 77 and uses MPI library for communications between nodes. The scalable properties of the program do not depend on the complexity of the studied system and are determined mainly by the hardware and communication speed. Examples of a few molecular systems differing by the composition will be given: Ionic water solutions, large DNA fragments in water solution with counter ions, a phospholipid membrane system.