GENESIS version 1.4
Download ver. 1.4.0
| Source code | Oct 31, 2019 | |
| User manual |
Oct 31, 2019 | |
| Test set | Oct 31, 2019 |
List of functions in ver. 1.4.0
- 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)
- Multi-dimensional REMD (T-REMD/REUS, gREST/REUS)
- Collective variable REUS
- String method
- Gaussian accelerated molecular dynamics method (GaMD, GaREUS)
- QM/MM calculation
- Anharmonic vibrational analysis (+SINDO)
- Cryo-EM flexible fitting
- 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
- Oct 31, 2019: GENESIS 1.4.0 released
- (ATDYN) Implicit solvent model (GBSA)
- (ATDYN) QM/MM calculation
- (ATDYN) Energy minimization (LBFGS, Micro-iteration)
- (ATDYN) Anharmonic vibrational analysis (+SINDO)
- (ATDYN) CHARMM C19
- (SPDYN) All-atom Go model
- (ATDYN, SPDYN) Cryo-EM flexible fitting
- (ATDYN, SPDYN) Gaussian accelerated MD
- (ATDYN, SPDYN) Repulsive distance restraint
- (ATDYN, SPDYN, Analysis) Distance-based atom selection
- (Analysis) Upgrade remd_convert, mbar_analysis, and wham_analysis
- (Analysis) Add trajectory analysis tools, mode analysis tools, converters, free energy analysis tools, interface, and other utilities