GENESIS

GENESIS version 1.7

Download ver. 1.7.1 

The license of GENESIS source code is the GNU Lesser General Public License version 3.

List of functions in ver. 1.7.1

• CHARMM force fields
  • CHARMM19, 22, 27, C36, C36m
• AMBER force fields
  • FF99SB (ATDYN/SPDYN), FF14SB (ATDYN/SPDYN), FF19SB (SPDYN) 
• MARTINI model
• Go models for protein
  
  • Cα and KB Go models
  • All-atom Go model
  • AICG2+ protein model 
  • Macro-mixing KB Go/DoME model 
• 3SPN.2C DNA model 
• Structure-based RNA model 
• HPS/KH model for IDR and RNA 
• PWMcos model for protein-DNA sequence-specific interaction 
• A tool for preparing CG files: GENESIS-CG-tool 
• Energy minimization
  • Steepest descent method
  • LBFGS
• Molecular dynamics simulation
  • Leapfrog, velocity Verlet, and RESPA integrators
  • NVE, NVT, NPT, NPAT, NPγT ensembles
  • Langevin, Berendsen, and Bussi thermostat/barostat
  • Particle mesh Ewald method
  • Constraints (SHAKE, RATTLE, SETTLE, LINCS)
  • Restraints (Position, distance, angle, dihedral, PCA)
  • Simulated annealing MD
  • Steered MD and Targeted MD
• Implicit solvent model
  • GB/SA model with CHARMM and AMBER force fields 
  • EEF1, IMM1, IMIC models
• Replica-exchange molecular dynamics method
  • Temperature, Pressure, Surface-tension REMD
  • Replica-exchange umbrella sampling (REUS or H-REMD)
  • Generalized replica exchange with solute tempering (gREST)
  • On-the-fly energy analysis in gREST
  • Multi-dimensional REMD (T-REMD/REUS, gREST/REUS)
  • Collective variable REUS
• Boundary
  • Periodic boundary condition (PBC)
  • Isolated system (no-PBC w/ or w/o spherical boundary potential)
• String method
• Gaussian accelerated molecular dynamics method (GaMD, GaREUS)
• QM/MM calculation
  • Minimization and vibrational analysis
  • Anharmonic vibrational analysis (+SINDO)
  • QM/MM molecular dynamics
  • Minimum energy path search using String methods
  • Supported QM software: Gaussian, Q-Chem, TeraChem, DFTB+, QSimulate-QM
  • Available MM force field: CHARMM and AMBER
• Cryo-EM flexible fitting
• Free-energy perturbation method (FEP) 
  • Hybrid topology scheme
  • Soft core potentials for non-bonded interactions
  • Lambda-exchange (Hamiltonian exchange) FEP
  • GPGPU acceleration
• Computation with working precision (Single/Double precision)
• GPGPU calculation in SPDYN
• TIP4P water model in SPDYN
• Trajectory analysis tools (Bond, Angle, Dihedral, RMSD, etc + 18 tools)
• Spatial decomposition analysis (SPANA)
• Morphing calculation(ATDYN)