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GENESIS 1.1: A hybrid‐parallel molecular dynamics simulator with enhanced sampling algorithms on multiple computational platforms
- Source :
- Journal of Computational Chemistry. 38:2193-2206
- Publication Year :
- 2017
- Publisher :
- Wiley, 2017.
-
Abstract
- GENeralized-Ensemble SImulation System (GENESIS) is a software package for molecular dynamics (MD) simulation of biological systems. It is designed to extend limitations in system size and accessible time scale by adopting highly parallelized schemes and enhanced conformational sampling algorithms. In this new version, GENESIS 1.1, new functions and advanced algorithms have been added. The all-atom and coarse-grained potential energy functions used in AMBER and GROMACS packages now become available in addition to CHARMM energy functions. The performance of MD simulations has been greatly improved by further optimization, multiple time-step integration, and hybrid (CPU + GPU) computing. The string method and replica-exchange umbrella sampling with flexible collective variable choice are used for finding the minimum free-energy pathway and obtaining free-energy profiles for conformational changes of a macromolecule. These new features increase the usefulness and power of GENESIS for modeling and simulation in biological research. © 2017 Wiley Periodicals, Inc.
- Subjects :
- 0301 basic medicine
Quantitative Biology::Biomolecules
010304 chemical physics
Computer science
String (computer science)
Graphics processing unit
General Chemistry
01 natural sciences
Power (physics)
Computational science
Modeling and simulation
03 medical and health sciences
Computational Mathematics
symbols.namesake
Molecular dynamics
Variable (computer science)
030104 developmental biology
0103 physical sciences
symbols
Umbrella sampling
Simulation
Gibbs sampling
Subjects
Details
- ISSN :
- 1096987X and 01928651
- Volume :
- 38
- Database :
- OpenAIRE
- Journal :
- Journal of Computational Chemistry
- Accession number :
- edsair.doi...........54793fcacb19079b8648d23934dca056