GENESIS version 1.6
Download ver. 1.6.0
Source code | Dec 23, 2020 | |
User manual |
Dec 23, 2020 | |
Test set | Dec 23, 2020 |
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.
List of functions in ver. 1.6.0
- 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
- Minimization and vibrational analysis
- Anharmonic vibrational analysis (+SINDO)
- QM/MM molecular dynamics
- Minimum energy path search using String/NEB methods
- 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)
- Dec 23, 2020: GENESIS 1.6.0 released
- (ATDYN) QM/MM MD
- (ATDYN) Minimum energy path search
- (TOOL) SPANA (sasa, rdf, density, hbond, contact)