PLAMS: Python Library for Automating Molecular Simulations¶
Table of contents
- Getting Started
- Examples
- Getting Started
- Molecule analysis
- PLAMS Molecule: store/load many file formats, convert to/from ASE, RDKit, pymatgen, and more
- Extract frames from ams.rkf trajectory
- Table molecule counts and bond count from reactive MD ams.rkf
- Molecule substitution: Attach ligands to substrates
- Convert to ams.rkf trajectory with bond guessing
- Correlation plots for output from different AMS jobs
- Convert RKF to DCD while mapping all atoms into molecules
- Hydrogen bonds from MD
- Plot molecular reactions
- MD trajectory analysis
- Benchmarks
- Workflows
- COSMO-RS and property prediction
- Packmol and AMS-ASE interfaces
- Packmol: Create liquids, gases, solid-liquid interfaces
- Engine ASE: AMS geometry optimizer with forces from any ASE calculator
- AMSCalculator: ASE geometry optimizer with AMS forces
- AMSCalculator: Access results files & Charged systems
- i-PI path integral MD with AMS
- Sella transition state search with AMS
- ParAMS, Simple Active Learning, and pyZacros
- Other AMS calculations
- Pymatgen
- Pre-made recipes
- ADF: Task COSMO-RS Compound
- Generating multiple conformers for use with COSMO-RS
- AMS Molecular Dynamics PLAMS jobs
- ADF fragment job
- Reorganization Energy
- NBO with ADF
- Numerical gradients
- Numerical Hessian
- Vibronic Density of States using the AH-FC method
- Vibronic Density of States with ADF
- Reuse ForceField Parameters
- Amsterdam Modeling Suite
- Components (Settings, Job, …)
- Cookbook
- init and finish
- Settings and input
- Create an input block with an header
- Create an empty input block
- Create an input block with repeating keys
- Repeating input block
- Create a “free” input block
- Convert an AMS text input into an AMS job
- Convert an AMS text input into settings object
- Convert an AMS .run file into an AMS job
- Specify paths to files in the input
- Restart from a previous job
- Molecules
- Extracting Results
- Accessing Old Jobs
- Parallelization
- Citations
- Other programs