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#

Molecular Dynamics

Molecular dynamics consists of solving Newton's equations of
motion
where the index runs through all free (i.e., not fixed) atoms and the gradient is derived from the X-PLOR energy function (Chapter 4). Presently, X-PLOR provides the option to solve Eq. 11.1 in Cartesian coordinate space (Section 11.1) or rigid-body coordinate space (Section 11.2). Molecular dynamics simulations can be stored as trajectory files. Input format, output format, manipulations, and analysis of trajectory files are described in Section 11.

**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*