GENESIS version 1.6


Download ver. 1.6.0
Source code Dec 23, 2020
User manual
Dec 23, 2020
Test set Dec 23, 2020

The license of GENESIS source code is changed from the GNU General Public License version 2 to the GNU Lesser General Public License version 3.


List of functions in ver. 1.6.0
  • 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/NEB methods
  • 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)