ORAC: A Molecular dynamics program to simulate complex molecular systems with realistic electrostatic interactions

TLDR

This study introduces ORAC, a new molecular dynamics program designed to efficiently simulate biomolecules in solution or crystalline environments. ORAC integrates advanced MD algorithms, including reversible symplectic multiple time step methods, Ewald and smooth particle mesh Ewald electrostatics, and support for multiple thermodynamic ensembles. The authors claim that ORAC’s algorithmic combination makes it more advanced than conventional MD programs. © 1997 John Wiley & Sons, Inc., J Comput Chem 18:1848–1862.

Abstract

In this study, we present a new molecular dynamics program for simulation of complex molecular systems. The program, named ORAC, combines state-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 crystalline environment. Among its unique features are: (i) implementation of reversible and symplectic multiple time step algorithms (or r-RESPA, reversible reference system propagation algorithm) specifically designed and tuned for biological systems with periodic boundary conditions; (ii) availability for simulations with multiple or single time steps of standard Ewald or smooth particle mesh Ewald (SPME) for computation of electrostatic interactions; and (iii) possibility of simulating molecular systems in a variety of thermodynamic ensembles. We believe that the combination of these algorithms makes ORAC more advanced than other MD programs using standard simulation algorithms. © 1997 John Wiley & Sons, Inc. J Comput Chem 18: 1848–1862, 1997