ORAC: A Molecular dynamics program to simulate complex molecular systems with realistic electrostatic interactions
✍ Scribed by Procacci, Piero; Darden, Tom A.; Paci, Emanuele; Marchi, Massimo
- Publisher
- John Wiley and Sons
- Year
- 1997
- Tongue
- English
- Weight
- 233 KB
- Volume
- 18
- Category
- Article
- ISSN
- 0192-8651
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✦ Synopsis
In this study, we present a new molecular dynamics program for simulation of complex molecular systems. The program, named ORAC, combines Ž . 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 Ž . features are: i implementation of reversible and symplectic multiple time step Ž . algorithms or r-RESPA, reversible reference system propagation algorithm specifically designed and tuned for biological systems with periodic boundary Ž . conditions; ii availability for simulations with multiple or single time steps of Ž . standard Ewald or smooth particle mesh Ewald SPME for computation of Ž . 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.