GENESIS version 2.1

Download ver. 2.1.1

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 Oct 2, 2023
User manual
Oct 2, 2023
Test set Oct 2, 2023

List of functions in ver. 2.1.1

  • CHARMM force fields
    • CHARMM19, 22, 27, C36, C36m
  • AMBER force fields
  • 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)
    • 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 2, 2023: GENESIS 2.1.1 released
    • Add energy_analysis for QM/MM calculation
    • Enable prediodic CV in pmf_analysis
    • (ATDYN/SPDYN) Update simd directive for Intel compiler version > 23.1
    • (ATDYN) Increase output frequency
    • (SPDYN) Update configure file for CUDA > 12.0
    • (ATDYN) Added QM interface with ORCA
    • (SPDYN) Bugfix: fix timing of transfer charge values to GPU card in gREST
    • (SPDYN) Bugfix: Ryckaert-Bellemans dihedral energy sum
    • (SPDYN) Bugfix: Virial term in amber bond correction was not written correctly and corrected.
    • (SPDYN) Bugfix: error in water number count is fixed in TIP4P case.
    • (ATDYN/SPDYN) BugFix: fix generation of random seed in replica simulations (REMD/RPATH)
    • (ATDYN/SPDYN) BugFix: fix wrong file name in large number of replicas
  • Feb 20, 2023: GENESIS 2.1.0 released
    • (SPDYN) Free-energy perturbation with modified Hamiltonian
    • Updates of Intel Fortran’s options for AMD CPU
    • Updates of regression test to prevent potential errors
Older versions

Download ver. 2.1.0

Source code Feb 20, 2023
User manual
Feb 20, 2023
Test set Feb 20, 2023