ASH: Documentation

These are the documentation pages of ASH, an open-source multiscale modelling program. The code is available on Github

ASH

• About ASH
  • Features
• Setup
  • A. Download ASH
  • B. Installation and Configuration
  • C. Install External Programs
  • D. Test ASH
  • E. Installation problems
• Basic usage
  • Input structure
  • Example script
  • Running script directly in the shell
  • Interactive ASH in a REPL or iPython environment
  • ASH with Julia support
  • ASH settings
  • Use of colors in ASH output
  • Submitting job
• Basic examples
  • Python basics
  • Defining coordinates in different ways
  • Defining theories
  • A few different job examples on H2O
• ASH Program Philosophy
  • Some basic principles we try to follow
• Coordinates and fragments
  • The Fragment class
  • Creating/modifying fragment objects
  • Direct creation of an ASH fragment from coordinates
  • Adding coordinates to object
  • Replace coordinates of object
  • Calculate connectivity of fragment object
  • Charge and Multiplicity
  • Label
  • Inspect defined fragment objects
• Parallelization in ASH
  • Job_parallel
  • Simple_parallel
• QM Interfaces
  • Attributes and methods available to all QM interfaces
• Scientific articles using ASH
  • MM and QM/MM protein studies
  • Highlevel WFT workflows

Jobtypes

• Job Types
  • Output object of ASH Job-types
  • Single-point calculation
  • Geometry optimization
  • Numerical frequencies (Hessian)
  • Analytical frequencies (Hessian)
  • Nudged Elastic Band Calculations
  • Surface scans
  • Saddle-point optimization
  • Molecular Dynamics
• Singlepoint
  • Singlepoint function
  • Singlepoint_fragments function
  • Singlepoint_theories function
  • Singlepoint_fragments_and_theories function
  • Singlepoint_reaction function
  • Singlepoint_parallel function
• Geometry optimization
  • geomeTRICOptimizer
  • Examples
  • Constraints
  • Convergence criteria
  • The geomeTRICOptimizer class
• Vibrational frequencies
  • Numerical frequencies
  • Analytical frequencies
  • thermochemistry corrections
  • Calculating IR and Raman spectra
• Molecular dynamics
  • Dynamics via OpenMM_MD
  • mdtraj interface
  • Dynamics via ASE
• Biased sampling MD & Free energy simulations
  • OpenMM_metadynamics
  • metadynamics_plot_data
  • Restraining CVs
  • Parallelization of metadynamics
  • Examples:
  • MTD_analyze (for Plumed run): Analyze the results
• Nudged Elastic Band
  • Recommendations and how to use
  • Examples
  • Controlling printout
  • Controlling guess orbitals during SCF of Theory level
  • Controlling convergence
  • Free-end NEB calculations
  • NEB on systems with an active region (e.g. QM/MM)
  • Parallelization
  • NEB-TS : combining CI-NEB with TS-optimization
• Surface Scan
  • Parallelization
  • How to use
  • Working with a previous scan from collection of XYZ files
  • Parallelization
  • Plotting

MM and Hybrid theories

• MM Interfaces
  • NonBondedTheory
  • OpenMM interface
• OpenMM interface
  • The OpenMMTheory class
  • Molecular Dynamics via OpenMM
  • PBC box relaxation via NPT
  • Simple minimization via OpenMM
  • Gentle WarmupMD
  • System setup via OpenMM: Modeller
  • Setting up a protein system with implicit solvation
  • Create forcefield for ligand / small molecule
  • write_nonbonded_FF_for_ligand
  • small_molecule_parameterizer
  • Small molecule solvation
• Hybrid Theory
  • Multilevel Theory Methods
  • DualTheory methods
• QM/MM Theory
  • QMMMTheory class
  • Defining the charge and spin multiplicity of the QM-region
  • Defining QM-region and active region
  • QM/MM boundary treatment
  • QM/MM Truncated PC approximation
  • Example: QM/MM with ORCA and NonbondedTheory
  • Example: QM/MM with ORCA and OpenMMTheory

Workflows

• Ensemble averaging
  • Wigner sampling
  • Examples:
• Electronic structure analysis
  • Creating and modifying Gaussian Cube files
  • Various analysis tools
  • NOCV analysis
  • Various ORCA-specific analysis tools
• Workflow functionality
  • Reaction class
  • ReactionEnergy
  • Thermochemprotocols
  • calc_xyzfiles: Run calculations on a collection of XYZ-files
• Highlevel workflows
  • ORCA_CC_CBS_Theory
  • ORCA_CC_CBS_Theory Examples
  • Reaction_Highlevel_Analysis
  • Reaction_FCI_Analysis
  • WFT theory with flexible orbital-input option
  • ICE-CI workflows
  • Automatic active-space selection
• Specific workflows
  • Counter-poise correction (ORCA)
  • Automatic non-Aufbau calculator
• Benchmarking in ASH
  • Available benchmarking options
  • The run_benchmark function
  • Running a test set with a chosen QMtheory
  • Running a test set with a highlevel theory workflow
  • Creating or modifying a test set
• MOLCRYS: Automatic QM/MM for Molecular Crystals
  • MOLCRYS function: Creating a cluster
  • MOLCRYS Example: Spherical QM/MM Cluster setup from CIF-file
  • MOLCRYS: QM/MM Geometry optimization
  • MOLCRYS: Expanded QM region calculation
  • MOLCRYS: Property calculation
  • MOLCRYS: Reaction path and saddle-point finding via NEB method
  • MOLCRYS: Numerical QM/MM frequencies
  • MOLCRYS: Fragment identification/Connectivity issues
  • MOLCRYS: Molecular Dynamics
• PES: PhotoElectron/PhotoEmission Spectrum
  • PhotoElectronSpectrum function
  • Plot spectrum
  • Example: TDDFT on H₂O
  • Example: FeS₂ ^- : TDDFT vs. IP-EOM-CCSD vs. CASSCF vs. MRCI+Q
• Plotting
  • ASH_plot: Basic plotting
  • plot_Spectrum: Plotting broadened spectrum
  • MOplot_vertical: Plot vertical MO diagram
  • Reaction_profile
  • Contour_plot

Interfaces

• ORCA interface
  • Finding the ORCA program
  • Examples
  • Parallelization
  • ORCA_External_Optimizer
  • Wrapper around ORCA helper programs.
  • ORCA fragment guess
  • Useful ORCA functions
  • Useful ORCA workflows
• xTB interface
  • Finding the xTB program
  • Examples
  • Parallelization
• MRCC interface
  • Finding the MRCC program
  • Using the interface
  • Parallelization
  • Examples
• CFour interface
  • Installation
  • Finding the CFour program
  • CC modules
  • Parallelization
  • Examples
• Dalton interface
• PySCF interface
  • PySCF installation
  • Parallelization
  • Examples
• Dice interface
  • Installing Dice
  • Using the interface
  • Parallelization
  • Examples
• Psi4 interface
• CREST interface
  • Example workflow 1. Call crest to get low-energy conformers as ASH fragments.
  • confsampler_protocol : Automatic Crest+DFTopt+DLPNO-CCSD(T) workflow
• QUICK interface
  • QUICK installation
  • QUICK performance control and parallelization
  • Examples
• NWChem interface
  • NWChem installation
  • Parallelization
  • Examples
• TeraChem interface
• Multiwfn interface

Tutorials

• Explicit solvation (small molecule)
  • Creating a small-molecule forcefield
  • Example 1. Modelling of an organic molecule in explicit water with a ligand forcefield
  • Example 2. Modelling of an inorganic molecule in explicit water using a simple non-bonded forcefield
  • Issues
• Metalloprotein tutorial I: Rubredoxin
  • 1. Use OpenMM_Modeller to set up the system
  • 2a. Minimize system and run a classical MD simulation
  • 2b. Run through an advanced NPT equilibration + long NVT simulation
  • 3. Run semi-empirical GFN-xTB QM/MM MD simulation
  • 4. Run QM/MM geometry optimizations at the DFT-level using ORCA as QM theory
• Metalloprotein tutorial II: Ferredoxin
  • 1. OpenMM_Modeller PDB parsing errors
  • 2. OpenMM residue variants: protonation states
  • 3. A more realistic nonbonded model for the [2Fe-2S]
  • 4. Classical MD simulation
• Metadynamics in ASH: Tutorial
  • 1. Single-CV metadynamics on n-butane
  • 2. 2-CV metadynamics on 3F-GABA in continuum solvent and QM/MM
  • 2. Metadynamics on a protein using MM and QM/MM
• Modelling protein-ligand binding in ASH: Tutorial
  • 1. Preparing initial files
  • 2. Preparing ligand forcefield
  • 3. Prepare system using OpenMM_Modeller
  • 4. Run initial preparatory MD simulations
  • 5. Run long time-scale NVT simulation
  • 6. Funnel metadynamics of the protein-ligand system
  • 7. QM/MM of the protein-ligand system
• QM/MM on a protein
  • 1. Prepare a classical MM model of the system.
  • 2a. Read coordinates and forcefield into ASH
  • 3. Create the QM/MM model and test it by running an energy calculation
  • 4. Run a QM/MM geometry optimization
  • 5. Modifying the coordinates of the QM-region
  • 6. Adding/removing atoms of the system
  • 7. Other QM/MM jobtypes
  • 8. EXAMPLE: Protein-setup, Opt, MD, QM/MM all in one script
• Workflow examples in ASH
  • Example 1 : Optimization + Frequency + HighLevel-singlepoint
  • Example 2a : Direct calculation of Reaction Energy: N₂ + 3H₂ → 2NH₃
  • Example 2b : Direct calculation of Reaction Energy with an Automatic Thermochemistry Protocol
  • Example 3a : Running multiple single-point energies with different functionals (sequential)
  • Example 3b : Running multiple single-point energies with different functionals (in parallel)
  • Example 4a : Running single-point energies on a collection of XYZ files (sequential)
  • Example 4b : Running single-point energies on a collection of XYZ files (parallel)
  • Example 5 : Calculate localized orbitals and create Cube files for multiple XYZ files or an XYZ-trajectory
  • Example 6 : Running conformer-sampling, geometry optimizations and High-level single-points
• Tutorial: High-level CCSD(T)/CBS workflows
  • Example: CCSD(T)/CBS for the N2 total energy and Bond Dissociation Energy
  • Example: Atomization energy and formation enthalpy of Methane
  • Example: CCSD(T) and DLPNO-CCSD(T)/CBS calculations on threshold energy of chlorobenzene
  • Example: DLPNO-CCSD(T)/CBS 3d Transition metal complex: Ionization of Ferrocene
  • Example: DLPNO-CCSD(T)/CBS calculations on a 4d Transition metal complex
• Tutorial: High-level wavefunction and density analysis
  • The nature of the problem
  • Densities for correlated WF methods
  • Analysis of the dipole moment
  • Population analysis
  • Difference density analysis
  • ELF analysis

Tools

• Coordinates and fragment tools
  • Modifying coordinates in ASH calculations
  • Define an active region
  • Adding/removing atoms of an MM system
  • Working with PDB files

Warning

This is ASH version 0.9. Use at your own risk!

Indices and tables

• Index

• Module Index

• Search Page