What is GENESIS?

All-atom MD simulation of Mycoplasma cytoplasm

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.

MD trajectories obtained by GENESIS can be visualized with VMD and other software. CHARMM-GUI input generator can be used for the preparation of GENESIS input files.

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.