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