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

ASH
Jobtypes
MM and Hybrid theories
- MM Interfaces
- 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
- QM/MM Theory
Workflows
- Ensemble averaging
- Electronic structure analysis
- Workflow functionality
- Highlevel workflows
- Specific workflows
- Benchmarking in ASH
- 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
- Plotting
Interfaces
Tutorials
- Explicit solvation (small molecule)
- Metalloprotein tutorial I: Rubredoxin
- Metalloprotein tutorial II: Ferredoxin
- Metadynamics in ASH: Tutorial
- Modelling protein-ligand binding in ASH: Tutorial
- 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
Tools
Warning
This is ASH version 0.9. Use at your own risk!