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Subsections

Boundary Conditions

In addition to periodic boundary conditions, NAMD provides spherical and cylindrical boundary potentials to contain atoms in a given volume. To apply more general boundary potentials written in Tcl, use tclBC as described in Sec. 9.11.

Periodic boundary conditions

NAMD provides periodic boundary conditions in 1, 2 or 3 dimensions. The following parameters are used to define these boundary conditions.

Spherical harmonic boundary conditions

NAMD provides spherical harmonic boundary conditions. These boundary conditions can consist of a single potential or a combination of two potentials. The following parameters are used to define these boundary conditions.

Cylindrical harmonic boundary conditions

NAMD provides cylindrical harmonic boundary conditions. These boundary conditions can consist of a single potential or a combination of two potentials. The following parameters are used to define these boundary conditions.


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