What is GENESIS?
- GENESIS (GENeralized-Ensemble SImulation System) is molecular dynamics and modeling software for bimolecular systems such as proteins, lipids, glycans, and their complexes. GENESIS is open source software distributed under the GPLv2 license.
- GENESIS works on typical Linux workstations, cluster machines, and massively-parallel supercomputers such as K computer at RIKEN. GPGPU calculation with CUDA enabled NVIDIA Graphics Cards is also available.
- GENESIS has been developed by the Computational Biophysics Research Team in RIKEN Advanced Institute for Computational Science (AICS), Japan.
Functions of GENESIS
The GENESIS program package is composed of two MD programs (ATDYN, SPDYN) and trajectory analysis tools.
- MD, Replica Exchange MD (REMD), Energy minimization
- CPUs+GPGPUs hybrid MD/REMD simulations
- Highly parallelized PME method
- Forcefields: AMBER, CHARMM C27 & C36, Go models (Cα, all-atom, and KB Go models), etc.
- High performance MD simulations of protein solution and membrane systems by CPUs/CPUs+GPGPUs
- Scalable MD simulations of huge systems (> 100,000,000 atoms) on massively parallel environment (such as K computer)
- Multi-dimensional REMD calculations; temperature, pressure, surface tension, umbrella sampling
- String method for most probable pathway search
- Umbrella sampling, Replica Exchange Umbrella Sampling (REUS), and string method in collective variable space
- NVE, NVT, NPT, NPAT, NPγT ensembles & Langevin, Berendsen, and Bussi thermostat and barostat
- Analysis: RMSD, RMSF, PCA, WHAM, MBAR, etc.
How to cite GENESIS
Any published work which uses GENESIS 1.0 or before might include the reference:
J. Jung, T. Mori, C. Kobayashi, Y. Matsunaga, T. Yoda, M. Feig, and Y. Sugita, WIREs Comput. Mol. Sci., 5, 310-323 (2015).
Any published work which use GENESIS 1.1.x should cite the following reference:
C. Kobayashi, J. Jung, Y. Matsunaga, T. Mori, T. Ando, K. Tamura, M. Kamiya, and Y. Sugita, J. Compute. Chem. 38, 2193-2206 (2017) (DOI: 10.1002/jcc.24874).
In computational neural science, there is another GENESIS (General Neuron Simulation System), which has a long history of the development. Our GENESIS has been developed independently in the computational structural biology field.