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Cartesian Coordinate Space

Normally, all atoms are free to move during molecular
dynamics. However, atoms can be fixed by using the
constraints fix statement (Section 8.1).
The atomic masses are defined through the topology statement
(Section 3.1.1). The initial atomic coordinates are
taken from the main coordinate set (atom properties X,Y,Z).
After completion of the desired molecular dynamics steps,
the main coordinate
set contains the coordinates of the last step. The initial velocities
are determined by various velocity assignment options or
can be set explicitly by using the vector statement
for the atom properties VX, VY, VZ. After
completion of the molecular dynamics run, the velocities of the
last step are stored in the atom properties VX, VY, VZ.
The SHAKE method (Section 8.2) can be used during molecular
dynamics to constrain specified distances, such as bond lengths.
After completion of the molecular dynamics calculation, the partial energy terms for the last molecular dynamics step are stored in the appropriate symbols. The name of the symbols is given by $energy-term (see Section 4.5). The overall energy (Eq. 4.1) is stored in the symbol $ENER; the rms gradient is stored in $GRAD. The value of the second energy function (Eq. 4.26) is returned in the symbol $PERT. In addition, the following symbols are declared: $TEMP, $TOTE, and $TOTK, which are respectively the temperature, total energy, and kinetic energy. If the IPRFRQ frequency is nonzero, the average values of the energy terms and the temperature are stored in symbols whose names are preceeded by “AVE "; e.g., the average bond energy is stored in the symbol $AVE BOND. These averages are computed over the whole molecular dynamics run.

**Subsections**

- 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

*Xplor-NIH 2024-09-13*