ORAC - A MOLECULAR-DYNAMICS PROGRAM TO SIMULATE COMPLEX MOLECULAR-SYSTEMS WITH REALISTIC ELECTROSTATIC INTERACTIONS

In this study, we present a new molecular dynamics program for simulat ion of complex molecular systems. The program, named ORAC, combines st ate-of-the-art molecular dynamics (MD) algorithms with flexibility in handling different types and sizes of molecules. ORAC is intended for simulations of molecular systems and is specifically designed to treat biomolecules efficiently and effectively in solution or in a crystall ine environment. Among its unique features are: (i) implementation of reversible and symplectic multiple time step algorithms (or r-RESPA, r eversible reference system propagation algorithm) specifically designe d and tuned for biological systems with periodic boundary conditions; (ii) availability for simulations with multiple or single time steps o f standard Ewald or smooth particle mesh Ewald (SPME) for computation of electrostatic interactions; and (iii) possibility of simulating mol ecular systems in a variety of thermodynamic ensembles. We believe tha t the combination of these algorithms makes ORAC more advanced than ot her MD programs using standard simulation algorithms. (C) 1997 John Wi ley & Sons, Inc.