Premium
ORAC: A Molecular dynamics program to simulate complex molecular systems with realistic electrostatic interactions
Author(s) -
Procacci Piero,
Darden Tom A.,
Paci Emanuele,
Marchi Massimo
Publication year - 1997
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/(sici)1096-987x(19971130)18:15<1848::aid-jcc2>3.0.co;2-o
Subject(s) - molecular dynamics , periodic boundary conditions , flexibility (engineering) , computer science , computation , electrostatics , ewald summation , variety (cybernetics) , statistical physics , computational science , chemistry , computational chemistry , algorithm , boundary value problem , physics , artificial intelligence , mathematics , statistics , quantum mechanics
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