title: Hybrid MPI/OpenMP Implementation of the ORAC Molecular Dynamics Program for Generalized Ensemble and Fast Switching Alchemical Simulations.
abstract: We present a new release (6.0β) of the ORAC program [Marsili et al. J. Comput. Chem. 2010, 31, 1106-1116] with a hybrid OpenMP/MPI (open multiprocessing message passing interface) multilevel parallelism tailored for generalized ensemble (GE) and fast switching double annihilation (FS-DAM) nonequilibrium technology aimed at evaluating the binding free energy in drug-receptor system on high performance computing platforms. The production of the GE or FS-DAM trajectories is handled using a weak scaling parallel approach on the MPI level only, while a strong scaling force decomposition scheme is implemented for intranode computations with shared memory access at the OpenMP level. The efficiency, simplicity, and inherent parallel nature of the ORAC implementation of the FS-DAM algorithm, project the code as a possible effective tool for a second generation high throughput virtual screening in drug discovery and design. The code, along with documentation, testing, and ancillary tools, is distributed under the provisions of the General Public License and can be freely downloaded at www.chim.unifi.it/orac .
authors.affiliation: Department of Chemistry, University of Florence , Sesto Fiorentino, 50019, Italy.
authors.forename: Piero
authors.initials: P
authors.lastname: Procacci
mesh_terms: D000465:Algorithms; D008024:Ligands; D056004:Molecular Dynamics Simulation; D004364:Pharmaceutical Preparations / Q000378:metabolism; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry / Q000378:metabolism; D012984:Software; D013816:Thermodynamics; D013997:Time Factors
chemical_list: D008024:Ligands; D004364:Pharmaceutical Preparations; D011506:Proteins