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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 2025-03-21