GENESIS version 1.2


Download ver. 1.2.1
Source code
Feb 7, 2018
User manual
Feb 7, 2018
Test set Feb 7, 2018

List of functions in ver. 1.2.1
  • 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)

Change log

  • Feb 7, 2018: GENESIS 1.2.1 released
    • (spdyn) Fix constraints on minimization
    • (atdyn) Fix dispersion correction for AMBER FF
    • (atdyn/spdyn) Fix memory allocation bug in off-grid REUS (if # of restraints in off-grid REUS > # of replicas)
    • (general) extend maximum characters per line in control file (for recent CHARMM-GUI)
  • Jan 19, 2018: GENSIS 1.2.0 released
    • source tree structure is modified
    • (spdyn) TIP4P water model enabled (AMBER/CHARMM)
    • (spdyn) minor bugfixes on domain specification
    • (atdyn/spdyn) minor fixes for rpath parameters
    • (build) support parallel compilation (e.g. make -j4)
    • (build) enable_debug=4 enabled for gfortran
Older versions
Source code
Jan 19, 2018
User manual
Jan 19, 2018