Download ver. 1.7.1 

( TODO: add a download link here? )

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

List of functions in ver. 1.7.1

  • CHARMM force fields
    • CHARMM19, 22, 27, C36, C36m
  • AMBER force fields
    • FF99SB (ATDYN/SPDYN), FF14SB (ATDYN/SPDYN), FF19SB (SPDYN) 
  • MARTINI model
  • Go models for protein
    • Cα and KB Go models
    • All-atom Go model
    • AICG2+ protein model 
    • Macro-mixing KB Go/DoME model 
  • 3SPN.2C DNA model 
  • Structure-based RNA model 
  • HPS/KH model for IDR and RNA 
  • PWMcos model for protein-DNA sequence-specific interaction 
  • A tool for preparing CG files: GENESIS-CG-tool 
  • 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
    • Constraints (SHAKE, RATTLE, SETTLE, LINCS)
    • Restraints (Position, distance, angle, dihedral, PCA)
    • Simulated annealing MD
    • Steered MD and Targeted MD
  • Implicit solvent model
    • GB/SA model with CHARMM and AMBER force fields
    • EEF1, IMM1, IMIC models
  • 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)
  • Morphing calculation(ATDYN)

Change log

  • Dec 10, 2021
    • (SPDYN) Introduce AMBER FF19SB
    • (ATDYN) Introduce AMBER GBSA model
    • (SPDYN) Fix FEP
    • (ATDYN) Fix GBSA
    • (ATDYN) Fix CG model
    • (ATDYN) Fix QM/MM
  • Nov 17, 2021:  Corrected the description of QM/MM and updated the manual.
  • Oct 6, 2021: GENESIS 1.7.0 released
    • (ATDYN) AICG2+ CG model for protein
    • (ATDYN) Macro-mixing KB Go/DoME model
    • (ATDYN) 3SPN.2C CG model for DNA
    • (ATDYN) Structure-based CG model for RNA
    • (ATDYN) HPS/KH CG model for IDR and RNA
    • (ATDYN) PWMcos CG model for protein-DNA sequence-specific interaction
    • (ATDYN) Morphing calculation
    • (Analysis) CG topology/parameter/coordinate generation: GENESIS-CG-tool
    • (Analysis) Q-value analysis for CG models
    • (Analysis) Extracting averages of selected atoms

Updated: