GENESIS version 2.0


Download ver. 2.0.3

Method 1: Get code from Github

The source code, test set, and user manual are available from GitHub.
* Click the “Code” bottom and select “Download ZIP” in the page.

Method 2: Download from this site
Source code Dec 27, 2022
User manual
Dec 27, 2022
Test set Dec 27, 2022


List of functions in ver. 2.0.3

  • 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 27, 2022
    • (SPDYN) Fix solute list allocation in gREST (Bugfix)
  • Dec 20, 2022
    • (SPDYN) Fix local restraints (Bugfix)
  • Dec 19, 2022
    • Fix regression tests for Fugaku
    • (SPDYN) Fix local restraints (Adding Error check, bugfix)
    • (SPDYN) Fix structure check
Older versions
Download ver. 2.0.2
Source code Dec 20, 2022
User manual
Dec 20, 2022
Test set Dec 20, 2022

 

Download ver. 2.0.1

Source code Dec 19, 2022
User manual
Dec 19, 2022
Test set Dec 19, 2022

 

Download ver. 2.0.0

Source code Jul 27, 2022
User manual
Jul 27, 2022
Test set Jul 27, 2022