GENESIS version 2.0 (Latest pre-release)


Download ver. 2.0 beta

The source code and user manual are available from GitHub.
* Click the “Code” bottom and select “Download ZIP” in the page.


List of functions in ver. 2.0 beta

Only SPDYN is available currently.
For the other functions that are not implemented in ver. 2.0 beta, please use ver. 1.7.

  • CHARMM and AMBER force fields
  • Energy minimization
    • Steepest descent method
  • Molecular dynamics simulation
    • Velocity Verlet, and RESPA integrators
    • NVE, NVT, NPT ensembles
    • Bussi thermostat/barostat
    • Particle mesh Ewald method
    • Constraints (SHAKE, RATTLE, SETTLE)
    • Restraints (Position, distance, angle, dihedral, PCA)
    • Simulated annealing MD
    • Steered MD and Targeted MD
  • Replica-exchange molecular dynamics method
    • Temperature, Pressure, Surface-tension REMD
    • Replica-exchange umbrella sampling (REUS or H-REMD)
    • Generalized replica exchange with solute tempering (gREST)
    • On-the-fly energy analysis in gREST
    • Multi-dimensional REMD (T-REMD/REUS, gREST/REUS)
    • Collective variable REUS
  • Boundary
    • Periodic boundary condition (PBC)
  • String method
  • Gaussian accelerated molecular dynamics method (GaMD, GaREUS)
  • Computation with working precision (Single/Double precision)
  • GPGPU calculation in SPDYN
  • TIP4P water model in SPDYN