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.

ORAC: A Molecular Dynamics Program to Simulate Complex Molecular Systems with Realistic Electrostatic Interactions / P. PROCACCI; PACI E.; T. DARDEN; M. MARCHI. - In: JOURNAL OF COMPUTATIONAL CHEMISTRY. - ISSN 0192-8651. - STAMPA. - 18:(1997), pp. 1848-1862.

ORAC: A Molecular Dynamics Program to Simulate Complex Molecular Systems with Realistic Electrostatic Interactions

PROCACCI, PIERO;
1997

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
18
1848
1862
P. PROCACCI; PACI E.; T. DARDEN; M. MARCHI
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Utilizza questo identificatore per citare o creare un link a questa risorsa: https://hdl.handle.net/2158/219739
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