GENESIS version 1.3
Download ver. 1.3.0
| Source code | Jun 18, 2018 | |
| User manual |
Jun 18, 2018 | |
| Test set | Jun 18, 2018 |
List of functions in ver. 1.3.0
- MD, REMD, and Minimization
- Computation with working precision (Single/Double precision)
- GPGPU calculation in SPDYN
- CHARMM C27, C36 force fields
- AMBER force fields
- MARTINI force fields
- Go models (Cα, all-atom, and KB Go models)
- Particle mesh Ewald method
- Restraints (Position, distance, angle, dihedral, and PCA)
- Constraints (SHAKE, SETTLE, RATTLE)
- Leapfrog Verlet and Velocity Verlet integrators
- RESPA integrator
- NVE, NVT, NPT, NPAT, NPγT ensembles
- Langevin thermostat and barostat
- Berendsen thermostat and barostat
- Bussi thermostat and barostat
- Temperature, Pressure, Surface-tension REMD
- Replica-exchange umbrella sampling (REUS or H-REMD)
- Collective variable REUS
- Multi-dimensional REMD
- String method
- String method on Cartesian space
- Simulated annealing MD
- Steered MD and Targeted MD
- Trajectory analysis tools (Bond, Angle, Dihedral, RMSD)
- TIP4P water model (AMBER/CHARMM; spdyn only)
- Generalized replica exchange with solute tempering (gREST)
Change log
- Jun 18, 2018: GENESIS 1.3.0 released
- (spdyn/atdyn) Enable generalized replica exchange with solute tempering (gREST)
- (spdyn) Improvement of nonbonded energy in GPU usage
- (spdyn/atdyn) Enable options, pressure_virial/pressure_rmsd,including virial terms from position/rmsd restraints in pressure evaluations
- (spdyn) Fix setup of AMBER FF when constraint is not set
- (atdyn) Fix PC restraints for computational performance