List of functions in ver. 2.2.0

  • CHARMM force fields

    • CHARMM19, 22, 27, C36, C36m

  • AMBER force fields

    • FF99SB (ATDYN/SPDYN), FF14SB (ATDYN/SPDYN), FF19SB (SPDYN)

  • SPICA/pSPICA model

  • Structure-based (Go-like) models for protein

    • Cα and KB Go models

    • All-atom Go model

    • AICG2+ protein model

    • Macro-mixing KB Go/DoME model

  • Coarse-Grained (CG) models

    • 3SPN.2C DNA model

    • Structure-based RNA model

    • HPS/KH, CALVADOS, and Mpipi models for IDR and RNA

    • PWMcos model for protein-DNA sequence-specific interaction

    • iSoLFv2 model for lipid

    • 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 (BAOAB with half-step pressure), Berendsen/Bussi/NHC thermostat with MTK-style 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)

  • Adaptively biased molecular dynamics and its variants

    • Adaptively biased molecular dynamics (ABMD)

    • Multiple-walker ABMD (MW-ABMD)

    • Replica-exchange ABMD (RE-ABMD)

    • Bias-exchange ABMD (BE-ABMD)

    • Generalized replica exchange with solute tempering ABMD (gREST-ABMD)

  • 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)

    • Dual and hybrid topology schemes

    • Soft core potentials for non-bonded interactions

    • Modified Hamiltonian

    • 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

  • Oct 20, 2026: GENESIS 2.2.0 released

    • (ATDYN/SPDYN) Added adaptively biased molecular dynamics (ABMD) and its variants.

    • (CGDYN) Added as a new MD engine for coarse-grained simulations.

    • (ATDYN/CGDYN) Added Mpipi coarse-grained model for IDP and RNA.

    • (ATDYN) Added iSoLFv2 for coarse-grained lipid simulations.

    • (SPDYN) Added SPICA/pSPICA for explicit-water coarse-grained simulations.

    • (SPDYN) Added a new Langevin integrator based on the BAOAB scheme.

    • Added support for LLVM/Clang and NVIDIA compilers.

    • Added support for AMD GPUs.

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