Molecular Dynamics and Sampling
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Molecular Dynamics

This section groups examples that build and analyze trajectories,
estimate transport properties, or bias and explore dynamics.

* Molecular Dynamics with Python

* ReaxFF Density Equilibration

* Diffusion Coefficient Temperature Dependence

* Diffusion Coefficient Supercell Dependence

* Gasphase IR spectrum from Molecular Dynamics

* IR Spectrum of an H2O Dimer from MD

* i-PI Path Integral MD with AMS

* Molecule and Bond Counts from Reactive MD

* Extract Frames from an AMS Trajectory with PLAMS

* Convert from XYZ/OUTCAR to RKF

* Convert RKF Trajectory to DCD Format

* PLUMED Biasing in AMS Molecular Dynamics

* Basic MD Trajectory Analysis with PLAMS

* Hydrogen Bonds from MD

* Viscosity from MD with the Green-Kubo Formalism
