GENESIS version 2.1

Download ver. 2.1.2

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 26, 2023
User manual
Dec 26, 2023
Test set Dec 26, 2023

List of functions in ver. 2.1.2

  • 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

  • Dec 26, 2023: GENESIS 2.1.2 released
    • Some flags (!$omp simd, !$dir$) have been removed.
    • Auto-test scripts in regression_test directory have been fixed; now, relative path of the program binary can be typed.
    • Old versions of Gfortran (4.4.7-6.X.Y) are not supported.
    • Intel Fortran version 2021.7.1 is not supported.
    • sasa_analysis in sp_analysis has been fixed to be available for multiple compilers and architectures.
    • Some regression test sets of REMD and RPATH have been modified to be available for multiple compilers and architectures.
  • 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. 2.1.1

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

Download ver. 2.1.0

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