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Next: Cartesian Coordinate Space Up: XPLOR Interface Manual Previous: Example
Molecular Dynamics
Molecular dynamics consists of solving Newton's equations of
motion
where the index


Subsections
- Cartesian Coordinate Space
- Simple Langevin Dynamics
- Velocity Assignment
- Temperature Control
- Finite Difference Approximation
- Dynamics Restarts
- Syntax of the Dynamics Verlet Statement
- Requirements
- Example: Run a Standard Molecular Dynamics Simulation
- Example: Run a Molecular Dynamics Simulation with Temperature Coupling
- Example: Run a Slow-cooling Molecular Dynamics Simulation
- Example: Run Langevin Dynamics
- Rigid-Body Coordinate Space
- Initialization
- Iteration
- Syntax of the Dynamics Rigid Statement
- Requirements
- Example: Run a Rigid-Body Dynamics Simulation
- Internal Coordinate Space
Xplor-NIH 2024-09-13