Genesis

Description

genesis website  

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.

GENESIS (version 1.5 or later) is free software under the LGPLv3. Earlier versions (<=1.4) were distributed as free software under the GPLv2 license.

Environment Modules

Run module spider genesis to find out what environment modules are available for this application. Both cpu and gpu builds are available

System Variables

• HPC_GENESIS_DIR - installation directory
• HPC_GENESIS_BIN - executable directory

Citation

All publications and commercial products using genesis should cite the following references:

   1. C. Kobayashi, J. Jung, Y. Matsunaga, T. Mori, T. Ando, K. Tamura, M. Kamiya, and Y. Sugita, J. Compute. Chem. 38, 2193-2206 (2017).
   2. J. Jung, T. Mori, C. Kobayashi, Y. Matsunaga, T. Yoda, M. Feig, and Y. Sugita, WIREs Comput. Mol. Sci., 5, 310-323 (2015).