Welcome to AutoSolvate’s documentation!

Automated workflow to solvate molecules and run QM/MM trajectories

Description

This open-source package enables automated initial structure generation for explicitly solvated systems. This includes input file preparation. Additionally automated QM/MM trajectory generation and microsolvated cluster extraction is supported for the explicitly solvated systems. These features empower the user to rapidly generate large computational data sets.

AutoSolvate can be run in three ways:

1. graphical user interface (GUI)

2. command line interface (CLI)

3. Python API

Quickstart

1. To start using AutoSolvate, you may read the Installation page.

2. To learn to use the command line interface (CLI), you may read the Tutorial.

3. To learn to use the graphical user interface (GUI), you may read the GUI Tutorial.

4. To import AutoSolvate as a Python API, you may refer to the API Documentation.

Contents:

• Installation
  • Dependencies
  • From source
  • Conda install
  • Check
  • Trouble shooting
• Tutorial
  • Prerequisites
  • Example 1: Naphthalene in Water
  • Example 2: Naphthalene Radical in Chloroform
  • Example 3: Naphthalene in Acetonitrile (custom solvent)
• GUI Tutorial
  • Prerequisites
  • Step 1: Solvate system
  • Step 2: MD Simulation
  • Step 3: Microsolvated cluster extraction
• Advanced Tutorial
  • Advanced Example 1: Custom Solvent
  • Advanced Example 2: Automated recommendation of solvent-solute closeness
  • Advanced Example 3: Freeze the solute molecule structure
• API Documentation
  • autosolvate.startboxgen
  • autosolvate.solventBoxBuilder
  • autosolvate.solventBoxBuilder.build
  • autosolvate.solventBoxBuilder.getSolutePDB
  • autosolvate.solventBoxBuilder.getFrcmod
  • autosolvate.solventBoxBuilder.getHeadTail
  • autosolvate.solventBoxBuilder.writeTleapcmd1
  • autosolvate.solventBoxBuilder.createLib
  • autosolvate.solventBoxBuilder.writeTleapcmd_add_solvent
  • autosolvate.solventBoxBuilder.processPackmolPDB
  • autosolvate.solventBoxBuilder.packSLUSLV
  • autosolvate.solventBoxBuilder.writeTleapcmd_custom_solvated
  • autosolvate.solventBoxBuilder.createAmberParm
  • autosolvate.generatetrajs.startmd
  • autosolvate.generatetrajs.writeMMminInput
  • autosolvate.generatetrajs.writeMMheatInput
  • autosolvate.generatetrajs.writeMMNVEInput
  • autosolvate.generatetrajs.writeMMNPTInput
  • autosolvate.generatetrajs.runMM
  • autosolvate.generatetrajs.writeQMMMTemplate
  • autosolvate.generatetrajs.writeQMMMMinInput
  • autosolvate.generatetrajs.writeQMMMInput
  • autosolvate.generatetrajs.runQMMM
  • autosolvate.clustergen.clustergen
  • autosolvate.clustergen.startclustergen
• AutoSolvateWeb Job Parameters
• Citation