GENESIS version 1.5

Download ver. 1.5.1
Source code Sep 3, 2020
User manual
Test set Dec 10, 2021

The license of GENESIS source code is changed from the GNU General Public License version 2 to the GNU Lesser General Public License version 3. The user manual for 1.5.1 is currently being prepared. The usage of 1.5.1 is almost the same as 1.4.0 except for the free-energy perturbation (FEP) method. If you use the FEP method, see Tutorial 15.1.

List of functions in ver. 1.5.1
  • CHARMM and AMBER force fields
  • MARTINI model
  • Go models (Cα, all-atom, and KB Go models)
  • 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
    • GB/SA implicit solvent model
    • Constraints (SHAKE, RATTLE, SETTLE, LINCS)
    • Restraints (Position, distance, angle, dihedral, PCA)
    • Simulated annealing MD
    • Steered MD and Targeted MD
  • 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
  • Anharmonic vibrational analysis (+SINDO)
  • 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)

Change log

  • Sep 3, 2020: GENESIS 1.5.1 released
    • (ATDYN) Fix L-BFGS minimization
    • (SPDYN) Fix free-energy perturbation
    • (SPDYN) Enable local restraints in free-energy perturbation
    • (Analysis) Fix mbar_analysis
    • (Analysis) Stop energy_analysis if there is non-desired mixtures of solvent and solute in angle/dihed/improp/cmap
    • (general) extend maximum characters per line in control file (for recent CHARMM-GUI)
  • May 1, 2020: GENESIS 1.5.0 released
    • (ATDYN) Add spherical boundary potential for no-PBC systems
    • (ATDYN) Compile without using OpenMP
    • (SPDYN) On-the-fly energy analysis in gREST
    • (SPDYN) Free-energy perturbation
    • (ATDYN, SPDYN) Add an option to avoid shrinkage in string methods
    • (ATDYN, SPDYN) MRC/CCP4 format is available for the target cryo-EM density map file
Older versions
Source code
May 1, 2020
Test set Dec 10, 2021