This is technical documentation. See also: SCM Website | SCM Helpdesk | Pricing & Free trial

AMS Driver AMS Driver AMS Driver
  • Installation
    • Windows
    • Linux
    • MacOS
    • Package manager Install optional components
  • Tutorials
    • Getting started
    • All tutorials
  • AMS Driver
    • Geometry and System
    • Geometry Optimization
    • Molecular Dynamics
    • Nudged Elastic Band (NEB)
    • PES Exploration
    • PES Scan, Linear Transit
    • Transition State Search
    • Vibrational Spectroscopy
  • Engines
    • ADF Molecular DFT
    • BAND Periodic DFT
    • DFTB Semi-empirical
    • ForceField AMBER, UFF, APPLE&P...
    • GFNFF Force field
    • Hybrid QM/MM and mixed methods
    • ML Potential Machine Learning potentials
    • MOPAC Semi-empirical
    • Quantum ESPRESSO Periodic DFT
    • VASP Periodic DFT
    • ReaxFF Reactive force field
    • ASE engine Use any ASE calculator
  • Meso/Macro
    • COSMO-RS Thermodynamic properties of fluids
    • Bumblebee OLED device modeling
    • Microkinetics
    • Zacros Kinetic Monte Carlo
  • Tools
    • GUI Graphical User Interface
    • ParAMS Parametrization tool
    • Simple Active Learning On-the-fly training of ML
    • OLED Deposition and Properties Multiscale OLED modeling
    • Reactions Discovery Automatic reaction-discovery workflow
    • ACE Reaction Network Generation of reaction networks
    • Conformers Conformers generation
    • MD Trajectory Analysis Analysis of MD trajectories
    • ChemTraYzer2 Detect reactions from MD simulations
    • Utilities Various utility tools
  • Scripting
    • Python Scripting Examples Examples for Python scripting
    • PLAMS Python Library for Automating Molecular Simulations
    • amspython Python stack shipped with AMS
    • pyCRS Python Scripting with COSMO-RS
    • SCM Base Library Python library with core modules
    • reactmap Atom mapping between reactants and products
    • Command-line tools
    • ASE calculator
    • pyZacros Python Library Zacros (Kinetic Monte Carlo)
  • AMS2026.1
  • Other versions
  • AMS Driver
  • Index
  • General
  • Input, execution and output
    • AMSPipe protocol specification
  • Geometry, System definition
  • Structure and Reactivity, Molecular Dynamics
    • Single point calculations
    • Bond energy calculations
    • Geometry optimization
    • Transition state search
    • PES Scan, Linear Transit
    • Nudged Elastic Band (NEB)
    • Intrinsic Reaction Coordinate (IRC)
    • Excited state optimizations
    • Molecular dynamics
    • Trajectory replay
    • Grand Canonical Monte Carlo (GCMC)
    • Automated PES Exploration
  • Gradients, Hessian, Stress tensor, Elasticity
  • Vibrational Spectroscopy
  • Vibrationally resolved electronic spectra
    • AH-FC: Adiabatic Hessian Franck-Condon
    • VG-FC: Vertical Gradient Franck-Condon
  • Dipole moment, Polarizability, Bond orders, Orbital Energies
  • Engines
  • Utilities
    • AMSbatch
    • AtomTyping
    • Conformers
    • Trajectory Analysis
    • VCD Analysis: VCDtools
  • Appendices
  • Required citations
  • Examples
    • Example: Simple geometry optimization
    • Example: Two-stage geometry optimization with initial Hessian
    • Example: Periodic lattice optimization under pressure
    • Example: Phase Transition Due To External Nonuniform Stress
    • Example: Boron nitride optimization under external stress
    • Example: Graphene optimization under external stress
    • Example: Constrained optimizations
    • Example: TS search starting from initial Hessian
    • Example: PES scan and TS search for H2 on graphene
    • Nudged Elastic Band (NEB) Examples
    • Example: IRC for HCN
    • Example: TS and IRC for Claisen reaction
    • Example: Linear transit
    • Example: 2D PES scan
    • Example: PES scan for lattice degrees of freedom
    • Example: Basin Hopping for Ar 13 cluster
    • Example: PES Exploration, Process Search for alanine with PLAMS
    • Example: PES Exploration, Binding Sites for O on Pt 111
    • Example: Importing conformers into PES explorations
    • Example: Simple MD for H2
    • Example: MD for a box of water
    • Example: Lattice deformations in MD
    • Example: PLUMED spherical constraint on Ion-Water cluster
    • Example: MM/MM with constrained ion-water cluster in periodic water box
    • Example: Measuring the friction coefficient using NEMD
    • Example: Measuring the viscosity using NEMD
    • Example: Two QM/MM calculations with only MM interactions across periodic boundaries
    • Example: Trajectory replays for PES scans, NEB and MD calculations
    • Example: Mode Refinement
    • Example: Mode Tracking
    • Example: Vibronic-Structure Tracking
    • Example: Phonons for graphene
    • Example: Phonons with isotopes
    • Example: User-defined Brillouin zone for phonon dispersion
    • Example: Elastic tensor
    • Example: ASE calculator as a pipe worker
    • Example: AMS as a pipe worker
  • Keywords
  • KF output files
  • FAQ
  1. Documentation /
  2. AMS Driver /
  3. Structure and Reactivity, Molecular Dynamics

Structure and Reactivity, Molecular Dynamics¶

  • Single point calculations
  • Bond energy calculations
  • Geometry optimization
  • Transition state search
  • PES Scan, Linear Transit
  • Nudged Elastic Band (NEB)
  • Intrinsic Reaction Coordinate (IRC)
  • Excited state optimizations
  • Molecular dynamics
  • Trajectory replay
  • Grand Canonical Monte Carlo (GCMC)
  • Automated PES Exploration
Previous
Geometry, System definition
Next
Single point calculations

Copyright Software for Chemistry and Materials