Welcome to gridmaker’s documentation!

Overview:

• General Workflow
  • Optimization problem
  • Solution strategy
    • Important terms
    • Workflow steps
• Parameter-search Grid
  • Grid Indexing
  • Variations
    • Notation for Variations
    • Function-induced Variations
    • Variation Shifting
    • Cartesian Variation
    • Main Variation
    • Coupled Variation
    • The Parameter-search Grid
  • The List of Sampled Points
• Interaction Parameters
  • Lennard-Jones parameters
    • Atomtype Parameters
    • Standard-pairtype Parameters
    • 1,4-pairtype Parameters
  • Macro-based parameters
  • Custom parameters
• Systems and Topologies
  • GROMACS-compatible Systems
    • Template Topology
    • Replacement of Interaction Parameters
• Coordinates
  • Configuration-recycling Routines
    • Arbitrary Configuration
    • Protocol-based Configuration
  • Configuration-construction Routines
    • Pure-liquid Configuration
    • Solute-in-solvent Configuration
    • Slab Configuration
  • Mixed-type Routines
    • Slab-from-Liquid Configuration
• Protocols
  • Protocol Output
  • GROMACS-compatible General Protocol
    • Simulation Extensions
  • GROMACS-compatible Alchemical Protocol
    • Simulation Extensions
• Properties
  • Component and Composite Properties
  • Component Properties
    • Gmx-energy based Properties
    • Polarization-energy Correction
    • Free-energy Difference
    • Ensemble Averages and Uncertainties
  • Composite Properties
    • Density
    • Enthalpy of Vaporization
    • Surface-tension Coefficient
    • Free-energy Difference
  • References
• Surrogate Model
  • Linear/Cubic Interpolation
  • Gaussian Process Regression (GPR)
• Score
• Grid Shifting

Program Usage:

• Command-line
• Customization API
  • Usage
  • Systems
  • Protocols
  • Properties
  • Surrogate Model
  • Score Function
  • Grid Shifting
  • Logging
  • Utilitary Functions and Classes
• Input File
  • Global input parameters
  • Blocks
• Output Files
  • Basic file structure
    • Tokens
    • Files
    • GROMACS-compatible Systems
    • GROMACS-compatible General protocol
    • GROMACS-compatible Alchemical protocol
  • Log file
  • Stdout and Stderr
• Post-processing
• Restarting a run
• Validation mode

Example Applications:

• Tutorial
  • File structure
  • Parameter optimization
    • Input file
    • Running the job
    • Post-processing
  • Validation
    • Input file
    • Customization
    • Running the job
    • Post-processing
  • References

Indices and tables

• Index

• Search Page