The license of GENESIS source code is the GNU Lesser General Public License version 3.

List of functions in ver. 1.6.2

  • CHARMM and AMBER force fields
  • MARTINI model
  • Go models (Cα, all-atom, and KB Go models)
  • Energy minimization
    • Steepest descent method
    • LBFGS
  • Molecular dynamics simulation
    • Leapfrog, velocity Verlet, and RESPA integrators
    • NVE, NVT, NPT, NPAT, NPγT ensembles
    • Langevin, Berendsen, and Bussi thermostat/barostat
    • Particle mesh Ewald method
    • GB/SA implicit solvent model
    • Constraints (SHAKE, RATTLE, SETTLE, LINCS)
    • 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)
    • Isolated system (no-PBC w/ or w/o spherical boundary potential)
  • String method
  • Gaussian accelerated molecular dynamics method (GaMD, GaREUS)
  • QM/MM calculation
    • Minimization and vibrational analysis
    • Anharmonic vibrational analysis (+SINDO
    • QM/MM molecular dynamics
    • Minimum energy path search using String methods
    • Supported QM software: Gaussian Q-Chem TeraChem DFTB+ QSimulate-QM
    • Available MM force field: CHARMM and AMBER
  • Cryo-EM flexible fitting
  • Free-energy perturbation method (FEP) 
    • Hybrid topology scheme
    • Soft core potentials for non-bonded interactions
    • Lambda-exchange (Hamiltonian exchange) FEP
    • GPGPU acceleration
  • Computation with working precision (Single/Double precision)
  • GPGPU calculation in SPDYN
  • TIP4P water model in SPDYN
  • Trajectory analysis tools (Bond, Angle, Dihedral, RMSD, etc + 18 tools)
  • Spatial decomposition analysis (SPANA)

Change log

  • Dec 23, 2020: GENESIS 1.6.0 released
    • (ATDYN) QM/MM MD
    • (ATDYN) Minimum energy path search
    • (TOOL) SPANA (sasa, rdf, density, hbond, contact)
  • Aug 1, 2021: GENESIS 1.6.1 released
    • (ATDYN) QM/MM with AMBER force field
    • (ATDYN) Interface with QSimulate-QM
  • Sep 27, 2021: GENESIS 1.6.2 released
    • (SPDYN/ATDYN) Compiling and running GENESIS on Windows 10
    • (TOOL) Deprecate energy_analysis

Updated: