This version has the following updates.
- (ATDYN) AICG2+ CG model for protein
- (ATDYN) Macro-mixing KB Go/DoME model
- (ATDYN) 3SPN.2C CG model for DNA
- (ATDYN) Structure-based CG model for RNA
- (ATDYN) HPS/KH CG model for IDR and RNA
- (ATDYN) PWMcos CG model for protein-DNA sequence-specific interaction
- (ATDYN) Morphing calculation
- (Analysis) CG topology/parameter/coordinate generation: GENESIS-CG-tool
- (Analysis) Q-value analysis for CG models
- (Analysis) Extracting averages of selected atoms
This version has the following updates.
- Compiling and running GENESIS on Windows 10 under cygwin and MSMPI
- Deprecate energy_analysis (Please use analysis_grest in [REMD] on spdyn)
This version has the following updates.
- (ATDYN) QM/MM with AMBER force field
- (ATDYN) Interface with QSimulate-QM
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)
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.
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)
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 on November 20-22 at University of Warsaw in Poland (website). Thank you for your participation!
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)
