genesis¶
Description¶
GENESIS (GENeralized-Ensemble SImulation System) has been developed mainly by Sugita group in RIKEN, (Computational Biophysics Research Team (R-CCS), Theoretical Molecular Science Laboratory (CPR), and Laboratory for Biomolecular Function Simulation (BDR)) since 2009. Using GENESIS, molecular dynamics simulation and modeling of various biomolecular systems are possible with high performance. Multi-scale simulations with atomistic, coarse-grained, and QM/MM models are available together with enhanced sampling methods and other advanced simulation techniques.
Environment Modules¶
Run module spider genesis to find out what environment modules are available for this application.
Environment Variables¶
- HPC_GENESIS_DIR - installation directory
- HPC_GENESIS_BIN - executable program directory
Citation¶
If you publish research that uses megraft you have to cite it as follows:
Jung, J., Yagi, K., Tan, C., Oshima, H., Mori, T., Yu, I., Matsunaga, Y., Kobayashi, C., Ito, S., Ugarte La Torre, D. and Sugita, Y., 2024. GENESIS 2.1: High-Performance Molecular Dynamics Software for Enhanced Sampling and Free-Energy Calculations for Atomistic, Coarse-Grained, and Quantum Mechanics/Molecular Mechanics Models. The Journal of Physical Chemistry B.https://pubs.acs.org/doi/10.1021/acs.jpcb.4c02096
Categories¶
Physics