Examples of GENESIS Input File

Example control files for atdyn/spdyn

• Recommended main control parameters
  • For GENESIS ver. 1.4 or later
• Molecular dynamics (MD) and energy minimization
  • Energy minimization with positional restraints on protein heavy atoms
  • MD simulation in the NVE ensemble with the CHARMM, AMBER, and coarse-grained force fields
  • MD simulation in the NVT ensemble with Langevin, Berendsen, and Bussi thermostat
  • MD simulation in the NPT ensemble with Langevin, Berendsen, and Bussi thermostat and barostat
  • MD simulation of a biological membrane in the NPT, NPAT, and NPγT ensembles
  • MD simulation of a small peptide in vacuum in the canonical ensemble (atdyn only)
• Enhanced-sampling simulation
  • Temperature REMD simulation in the NVT and NPT ensembles
  • Pressure REMD simulation in the NPT ensemble
  • Surface-tension REMD simulation for a membrane system
  • Replica-exchange umbrella sampling (REUS or Hamiltonian REMD) using a distance restraint
  • Two-dimensional REMD (T-REMD/REUS) simulation

Example control files for analysis tools

• Structure analysis
  • RMSD: root-mean-square deviation (rmsd_analysis)
  • Distance, Angle, Dihedral angle, COM distance, COM angle, COM dihedral angle (trj_analysis)
  • Radius of gyration (rg_analysis)
  • Hydrogen bonds (hb_analysis)
  • Center of mass coordinates (comcrd_analysis)
  • Mean-square displacement (msd_analysis)
  • Diffusion constant (diffusion_analysis)
  • Distance-distance matrix (distmat_analysis)
  • RMSF: root-mean-square fluctuation (flccrd_analysis)
  • Membrane thickness (lipidthick_analysis)
  • Tilt angle of transmebrane helix (tilt_analysis)
  • Distance RMSD (drms_analysis)
  • Fraction of the native contacts (qval_analysis)
  • FRET efficiency (fret_analysis)
• Spatial decomposition analysis (SPANA)
  • General introduction of SPANA
  • Solvent accessible surface area (sasa_analysis)
  • Radial distribution function (rdf_analysis)
  • Density (density_analysis)
  • Hydrogen bonds (hbond_analysis)
  • Contact (contact_analysis)
• Principal component analysis
  • Calculation of the averaged coordinates (avecrd_analysis)
  • Calculation of the variance-covariance matrix (flccrd_analysis)
  • Diagonalization of the variance-covariance matrix (eigmat_analysis)
  • Projection of the coordinates trajectory onto PC axes (prjcrd_analysis)
  • Visualization of the PC vectors by VMD or PyMol (pcavec_drawer)
• Free energy calculations
  • WHAM: weighted histogram analysis method (wham_analysis)
  • MBAR: multistate Bennett acceptance ratio (mbar_analysis)
  • Free energy profile using MBAR output (pmf_analysis)
• Interface program
  • Protein secondary structure analysis by using the DSSP program (dssp_interface)
• Clustering
  • Structure clustering using the k-means algorithm (kmeans_clustering)
• Converter
  • Manipulate trajectories (combining, thinning, fitting, wrapping, centering, format change) (crd_convert)
  • Convert coordinates obtained from parallel I/O (pcrd_convert)
  • Sort coordinates and energy trajectories by replica parameters (remd_convert)
  • Convert GENESIS restart file to PDB file (rst_convert)
  • Convert restart file format from those in Ver. 1.0 to Ver. 1.1 or later (rst_upgrade)
• Other utilities
  • Generate inputs for string method calculation from Targeted MD data (rpath_generator)
  • Calculate tangential and orthogonal coordinates to a pathway from samples (pathcv_analysis)
  • Create synthetic EM density map from PDB file (emmap_generator)
  • Generate a system for QM/MM calculation from MD data (qmmm_generator)