GENESIS

• 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)

• 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

GENESIS 1.2.0 (Release date: Jan. 19, 2018)

• 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 (1.1.2 or later)
• Simulated annealing MD
• Steered MD and Targeted MD
• Trajectory analysis tools (Bond, Angle, Dihedral, RMSD)

• 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

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)

GENESIS 1.1.4 (Release date: Mar. 1, 2017)

GENESIS 1.1.3 (Release date: Feb. 24, 2017)

GENESIS 1.1.2 (Release date: Feb. 22, 2017)

GENESIS 1.1.1 (Release date: Sep. 07, 2016)

GENESIS 1.1.0 (Release date: Jul. 29, 2016)

GENESIS 1.0 (Release date: May 08, 2015)

List of functions in GENESIS 1.0:

• MD, REMD, and Minimization
• Computation with double precision
• CHARMM C27, C36 force fields
• Go models (Cα, all-atom, and KB Go)
• Particle mesh Ewald method
• Restraints (Position, distance, angle, dihedral)
• Constraints (SHAKE, SETTLE, RATTLE)
• Leapfrog Verlet and Velocity Verlet integrators
• NVE, NVT, NPT, NPAT, NPγT ensembles
• Langevin thermostat and barostat
• Berendsen thermostat and barostat
• Temperature, Pressure, Surface-tension REMD
• Replica-exchange umbrella sampling (REUS or H-REMD)
• Multi-dimensional REMD
• Simulated annealing MD
• Trajectory analysis tools (Bond, Angle, Dihedral, RMSD)

SFMT is a new variant of Mersenne Twister (MT) introduced by Mutsuo Saito and Makoto Matsumoto in 2006. The algorithm was reported at MCQMC 2006. The routine is distributed under the New BSD License.

© 2006,2007 Mutsuo Saito, Makoto Matsumoto and Hiroshima University.
© 2012 Mutsuo Saito, Makoto Matsumoto,
Hiroshima University and The University of Tokyo.

A Mersenne Twister random number generator was originally written in C by Makoto Matsumoto and Takuji Nishimura, and later translated into Fortran by Hiroshi Takano and Richard Woloshyn. This routine is distributed under the GNU General Public License version 2.

© 1997 Makoto Matsumoto and Takuji Nishimura.
© 1999 Hiroshi Takano.
© 1999 Richard Woloshyn.

FFTE is written by Daisuke Takahashi (Tsukuba University).

© 2000-2004, 2008-2011 Daisuke Takahashi (Tsukuba University).

You may use, copy, modify this code for any purpose (include commercial use) and without fee. You may distribute this ORIGINAL package.

A Complementary error function routine (erfc04) is written by SunSoft, a Sun Microsystems, Inc. business.

© 1993 Sun Microsystems, Inc.

Developed at SunSoft, a Sun Microsystems, Inc. business. Permission to use, copy, modify, and distribute this software is freely granted, provided that this notice is preserved.

See atdyn/at_energy_pme.fpp, and spdyn/sp_energy_pme.fpp for details.