Documentation 2019¶
General¶
- Installation Manual
- Installation of the Amsterdam Modeling Suite program package.
- Tutorials
- GUI-, Scripting- and Advanced tutorials for all programs.
Programs¶
- ADF (Amsterdam Density Functional)
A DFT program particularly strong in understanding and predicting structure, reactivity, and spectra of molecules.
- QM/MM
- Treat part of the atoms quantum-mechanically (QM) and the other ones by molecular mechanics (MM).
- ReaxFF
- SCM’s standalone version of the reactive force field approach developed by Prof. Adri van Duin and coworkers.
- AMS driver
The new driver program introduced in the 2018 release of the Amsterdam Modeling Suite.
- BAND
- BAND is an atomic-orbital based DFT program for periodic systems.
- DFTB
- DFTB (Density-Functional based Tight-Binding) is a fast approximate DFT.
- ReaxFF
- AMS version of the reactive force field approach developed by Prof. Adri van Duin and coworkers.
- UFF
- UFF (Universal Forcefield) is a molecular mechanics program for the full periodic table.
- MOPAC
- MOPAC is a general-purpose semiempirical molecular orbital package.
- ADF
- Use ADF as an AMS engine.
- GUI
- The Graphical User Interface.
- COSMO-RS
- COSMO-RS (COnductor like Screening MOdel for Realistic Solvents) is a program for calculating thermodynamic properties of (mixed) fluids.
- Quild
- QUILD (Quantum-regions Interconnected by Local Descriptions) enables calculations for multi-level approaches.
Scripting¶
- Scripting
- The ADF modelling suite includes several scripting environments, each with a specific scope and purpose.
- PLAMS
- PLAMS (Python Library for Automating Molecular Simulation) is a collection of tools that aim at providing powerful, flexible and easily extendable Python interface to molecular modeling programs.
Third party software¶
What’s new in AMS2019¶
AMS driver
The following new features in the AMS driver can be used in combination with any engine
- Grand Canonical Monte Carlo (GCMC)
- Intrinsic Reaction Coordinate (IRC) Scan
- Tools for mode selective vibrational analysis (Mode Scanning, Mode Refinement and Mode Tracking)
- Thermodynamic properties (ideal gas) from normal modes
- Partial Vibrational Spectra (PVDOS) for normal modes
- Molecular composition analysis for molecular dynamics simulations (see AMS-MD tutorial)
- Molecule gun and molecule sink for molecular dynamics
- PLUMED library support for MD analysis and a wide variety of free energy methods
- Collective Variable-driven Hyperdynamics (CVHD)
- Symmetry labels for normal modes and enforced symmetry in geometry optimizations.
GUI
- Polymer builder in ADFInput
- Calculation of spectra overlap (SimIR) and spectra overlap optimization in ADFSpectra.
- Centroids for in ADFInput
DFTB
- The GFN1-xTB method by Grimme et al. has been implemented in the DFTB engine for molecules and periodic systems (gamma-point only). GFN1-xTB orbitals can be visualized with ADFView.
- More robust SCC convergence
ADF
- New QTAIM and Conceptual DFT options
- AOResponse: polarizability and Raman spectra in combination with spin-orbit coupling
- DRF gradients (expert option)
BAND
MOPAC
- MOPAC has been fully integrated as an Engine in the Amsterdam Modeling Suite; this significantly speeds up the execution of MOPAC via AMS. Parallel MOPAC binaries. Several new input options.
ReaxFF
- ADFtrain: new GUI module for handling training sets and ReaxFF force field files (see tutorial on ReaxFF force field re-parametrization)
- OpenMP parallelization in ReaxFF
COSMO-RS