This version has the following updates.
- (ATDYN) QM/MM with AMBER force field
- (ATDYN) Interface with QSimulate-QM
Archives
GENESIS 2.0 beta3 is released
GENESIS 1.6.0 released
This version has the following updates.
- (ATDYN) QM/MM MD
- (ATDYN) Minimum Energy Path Search
- (Analysis) Spatial Decomposition Analysis (SPANA) (sasa, rdf, density, hbond, contact)
GENESIS 2.0 beta available
Ver. 2.0 beta is quite faster than ver. 1.X, and also optimized for the FUGAKU super-computer. Note that the available functions are currently limited to only SPDYN, since this is a pre-release version. For details, see the “Download” page.
GENESIS 1.5.1 released
This version has the following updates.
- (ATDYN) Fix L-BFGS minimization
- (SPDYN) Fix free-energy perturbation
- (SPDYN) Enable local restraints in free-energy perturbation
- (Analysis) Fix mbar_analysis
- (Analysis) Stop energy_analysis if there is non-desired mixtures of solvent and solute in angle/dihed/improp/cmap
- (general) extend maximum characters per line in control file (for recent CHARMM-GUI)
GENESIS 1.5.0 released
This version has the following new features.
- Free-energy perturbation method (FEP)
- On-the-fly energy analysis in gREST
- Isolated system (no-PBC w/ or w/o spherical boundary potential)
Joint tutorial of GENESIS, RedMDStream, and MINT was held in Poland!
Joint tutorial of GENESIS, RedMDStream, and MINT was held on November 20-22 at University of Warsaw in Poland (website). Thank you for your participation!
GENESIS 1.4.0 released!
This version has the following new features.
- Cryo-EM flexible fitting (REUSfit, MDfit)
- GB/SA implicit solvent model
- Hybrid QM/MM (quantum mechanics/molecular mechanics) calculation
- Energy minimization with LBFGS
- Anharmonic vibrational analysis (+SINDO)
- Gaussian accelerated molecular dynamics method (GaMD, GaREUS)
GENESIS 1.3.0 released
This version contains following bugfixes.
- (spdyn/atdyn) Enable generalized replica exchange with solute tempering (gREST)
- see Chap 14 REMD of the manual, web tutorial and FAQ.
- (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
GENESIS 1.2.1 released
This version contains following bugfixes.
- (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)