Welcome to Implicit_Solvent_DDM’s documentation!

Implicit_Solvent_DDM is a command-line interface for performing absolute binding free energy calculations. Currently, it supports only AMBER force fields and file formats .parm7 and .mol2.

Getting Started

Getting Started

• Installation
  • Usage
• Implementation Details
• Conformationally restrained Alchemical-Pathway
  • ISDMM.py Workflow
• DDM Workflow Structure
  • Overview
  • Simplified Workflow Flow
  • Workflow Phases
  • Detailed Module Interaction Flow
  • Module Descriptions
  • Related Documentation
• YAML Config Syntax
  • ABFE example:

Examples

Examples

• Running Basic MD at the endstate simulation
  • Running host-guest (CB7) absolute free energy calculation example:
• Running REMD at the endstate simulation
  • Running host-guest (CB7) absolute free energy calculation example:
• User Provided Endstate Simulation
  • Running host-guest (CB7) absolute free energy calculation example:

Software Documentation

Software Documentation

• API Documentation
  • implicit_solvent_ddm.implicit_ddm_workflow
  • implicit_solvent_ddm.workflow_phases
  • implicit_solvent_ddm.setup_simulations
  • implicit_solvent_ddm.runner.IntermidateRunner
  • implicit_solvent_ddm.run_endstate
  • implicit_solvent_ddm.config
  • implicit_solvent_ddm.matrix_order.CycleSteps
  • implicit_solvent_ddm.adaptive_restraints
  • implicit_solvent_ddm.alchemical
  • implicit_solvent_ddm.mdin
  • implicit_solvent_ddm.mdout
  • implicit_solvent_ddm.pandasmbar
  • implicit_solvent_ddm.postTreatment
  • implicit_solvent_ddm.restraint_helper
  • implicit_solvent_ddm.restraints
  • implicit_solvent_ddm.simulations
• Updates and Changelog
• Version 1.1.1 - GPU Acceleration Support
  • Major Features
• Version 1.0.0 - Initial Stable Release
  • Related Documentation
• About this package

Indices and Tables

• Index

• Module Index

• Search Page