GENESIS

GENESIS version 1.6

Download ver. 1.6.0

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)