GENESIS version 1.1


Download ver. 1.1.6
Source code
 Oct 17, 2017
Download (genesis-1.1.6.tar.bz2)
User manual
 Oct 27, 2017
Download (GENESIS-1.1.6.pdf)
Test set Oct 17, 2017
Download (tests-1.1.6.tar.bz2)

List of functions in ver. 1.1.6
  • MD, REMD, and Minimization
  • Computation with working precision (Single/Double precision) icon4neworange
  • GPGPU calculation in SPDYN icon4neworange
  • CHARMM C27, C36 force fields
  • AMBER force fields icon4neworange
  • MARTINI force fields icon4neworange
  • Go models (Cα, all-atom, and KB Go models)
  • Particle mesh Ewald method
  • Restraints (Position, distance, angle, dihedral, and PCA icon4neworange)
  • Constraints (SHAKE, SETTLE, RATTLE)
  • Leapfrog Verlet and Velocity Verlet integrators
  • RESPA integrator icon4neworange
  • NVE, NVT, NPT, NPAT, NPγT ensembles
  • Langevin thermostat and barostat
  • Berendsen thermostat and barostat
  • Bussi thermostat and barostat icon4neworange
  • Temperature, Pressure, Surface-tension REMD
  • Replica-exchange umbrella sampling (REUS or H-REMD)
  • Collective variable REUS icon4neworange
  • Multi-dimensional REMD
  • String method icon4neworange
  • String method on Cartesian space (1.1.2 or later)icon4neworange
  • Simulated annealing MD
  • Steered MD and Targeted MD icon4neworange
  • Trajectory analysis tools (Bond, Angle, Dihedral, RMSD)

Change log

  • Oct 27, 2017: minor update of manual
  • Oct 17, 2017: GENESIS 1.1.6 released
    • (spdyn) fix of GPU code for newer NVIDIA drivers (version > 380)
    • (configuration) fix of configure files
    • (atdyn/spdyn) enable restarting minimization
    • (atdyn) nonb_limiter is enabled
  • Jul 10, 2017: GENESIS 1.1.5 released
    • (atdyn/spdyn) Fix of R-path (string method)
    • (atdyn/spdyn) Fitting method (used in targeted MD, steered MD, string method etc.) renewal; [FITTING] section is introduced to extend the capability of structure fitting.
    • (manual) description concerning [FITTING] was added
    • (spdyn) improve GPU detection mechanism (automatically ignore GPUs with CC < 3.5)
    • (atdyn/spdyn) fix random generator used in BUSSI thermostat/barostat
    • (spdyn) fix for communication tag
    • (spdyn/tests) update of BUSSI NVT (regression test is also updated)
    • (atdyn/spdyn) fix of gromacs input for SMOG2
    • (atdyn/spdyn) fix of restart file reader (K-computer and FX100 only; there could be large delay when reading input files (not always))
    • (tests) test.py script now accepts relative path for the atdyn/spdyn executables
  • Jul 10, 2017: GENESIS 1.1.1-1.1.3 source codes were removed due to a potential license issue. (if you need them, please ask us via email.)
  • Jul 10, 2017: Source codes of 1.1.0 and 1.1.4 were updated to avoid a potential license issue
  • Mar 1, 2017: GENESIS 1.1.4 released
    • (spdyn) additional fix for OpenMP (1.1.2, 1.1.3 users should update to this version)
  • Feb 24, 2017: GENESIS 1.1.3 released
    • (spdyn) fix bug of contact_check when OpenMP thread number > 1 (not always)
    • unnecessary files and directories are removed (Feb 27, 2017; the removed files might be unharmful)
  • Feb 22, 2017: GENESIS 1.1.2 released
    • (spdyn) Cartesian coordinates can be employed as CV in the string method
    • (rpath_generator) improved functionality
    • (atdyn/spdyn) more smart handling of restart files
    • (spdyn) show GPU hardware information in log file
    • (spdyn) multiple GPUs in a single node can be used effectively in non-OpenMPI environment (such as Intel MPI)
    • (spdyn) structure_check is implemented in spdyn (runtime structure check upon pairlist generation)
    • (atdyn) support CHARMM19
  • Sep 07, 2016: GENESIS 1.1.1 released
    • (code) fix problems while installing with CUDA-8.0RC and single precision
    • (code) fix file I/O of the analysis tools (mbar_analysis, wham_analysis, pmf_analysis)
    • (code) change default of pme_alpha in the [ENERGY] section
    • (code) remove unnecessary error messages
    • (tests) set pme_alpha in the control files due to change of the default
  • Aug 23, 2016: (manual) fix sample of the [SELECTION] section (p.43)
  • Jul 29, 2016: GENESIS 1.1.0 released
Older versions

Source codes of GENESIS 1.1.1, 1.1.2, 1.1.3 were removed to avoid potential license issue. If you need source code of those versions, please ask us via e-mail or something. GENESIS 1.1.0 and 1.1.4 were also updated for the same reason. This update does not cause any changes in their functions and results of calculations. (Jul. 10, 2017)

GENESIS 1.1.5 (Release date: Jul. 10, 2017)
Source
 Jul 10, 2017
Download (genesis-1.1.5.tar.bz2)
Manual Jul 10, 2017
Download (GENESIS-1.1.5.pdf)
GENESIS 1.1.4 (Release date: Mar. 1, 2017)
Source
 Jul 10, 2017
Download (genesis-1.1.4.tar.bz2)
Manual Mar 1, 2017
Download (GENESIS-1.1.4.pdf)
GENESIS 1.1.3 (Release date: Feb. 24, 2017)
Source
 Feb 24, 2017  
Manual Feb 24, 2017
Download (GENESIS-1.1.3.pdf)
GENESIS 1.1.2 (Release date: Feb. 22, 2017)
Source
 Feb 22, 2017  
Manual Feb 22, 2017
Download (GENESIS-1.1.2.pdf)
GENESIS 1.1.1 (Release date: Sep. 07, 2016)
Source
 Sep 07, 2016  
Manual Sep 07, 2016
Download (GENESIS-1.1.1.pdf)
GENESIS 1.1.0 (Release date: Jul. 29, 2016)
Source
 Jul 10, 2017
Download (genesis-1.1.0.tar.bz2)
Manual Aug 23, 2016
Download (GENESIS-1.1.0.pdf)