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Subsections

## 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.

• sphericalBC use spherical boundary conditions?
Acceptable Values: on or off
Default Value: off
Description: Specifies whether or not spherical boundary conditions are to be applied to the system. If set to on, then sphericalBCCenter, sphericalBCr1 and sphericalBCk1 must be defined, and sphericalBCexp1, sphericalBCr2, sphericalBCk2, and sphericalBCexp2 can optionally be defined.

• sphericalBCCenter center of sphere (Å)
Acceptable Values: position
Description: Location around which sphere is centered.

• sphericalBCr1 radius for first boundary condition (Å)
Acceptable Values: positive decimal
Description: Distance at which the first potential of the boundary conditions takes effect. This distance is a radius from the center.

• sphericalBCk1 force constant for first potential
Acceptable Values: non-zero decimal
Description: Force constant for the first harmonic potential. A positive value will push atoms toward the center, and a negative value will pull atoms away from the center.

• sphericalBCexp1 exponent for first potential
Acceptable Values: positive, even integer
Default Value: 2
Description: Exponent for first boundary potential. The only likely values to use are 2 and 4.

• sphericalBCr2 radius for second boundary condition (Å)
Acceptable Values: positive decimal
Description: Distance at which the second potential of the boundary conditions takes effect. This distance is a radius from the center. If this parameter is defined, then spericalBCk2 must also be defined.

• sphericalBCk2 force constant for second potential
Acceptable Values: non-zero decimal
Description: Force constant for the second harmonic potential. A positive value will push atoms toward the center, and a negative value will pull atoms away from the center.

• sphericalBCexp2 exponent for second potential
Acceptable Values: positive, even integer
Default Value: 2
Description: Exponent for second boundary potential. The only likely values to use are 2 and 4.

### 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.

• cylindricalBC use cylindrical boundary conditions?
Acceptable Values: on or off
Default Value: off
Description: Specifies whether or not cylindrical boundary conditions are to be applied to the system. If set to on, then cylindricalBCCenter, cylindricalBCr1, cylindricalBCl1 and cylindricalBCk1 must be defined, and cylindricalBCAxis, cylindricalBCexp1, cylindricalBCr2, cylindricalBCl2, cylindricalBCk2, and cylindricalBCexp2 can optionally be defined.

• cylindricalBCCenter center of cylinder (Å)
Acceptable Values: position
Description: Location around which cylinder is centered.

• cylindricalBCAxis axis of cylinder (Å)
Acceptable Values: x, y, or z
Description: Axis along which cylinder is aligned.

• cylindricalBCr1 radius for first boundary condition (Å)
Acceptable Values: positive decimal
Description: Distance at which the first potential of the boundary conditions takes effect along the non-axis plane of the cylinder.

• cylindricalBCl1 distance along cylinder axis for first boundary condition (Å)
Acceptable Values: positive decimal
Description: Distance at which the first potential of the boundary conditions takes effect along the cylinder axis.

• cylindricalBCk1 force constant for first potential
Acceptable Values: non-zero decimal
Description: Force constant for the first harmonic potential. A positive value will push atoms toward the center, and a negative value will pull atoms away from the center.

• cylindricalBCexp1 exponent for first potential
Acceptable Values: positive, even integer
Default Value: 2
Description: Exponent for first boundary potential. The only likely values to use are 2 and 4.

• cylindricalBCr2 radius for second boundary condition (Å)
Acceptable Values: positive decimal
Description: Distance at which the second potential of the boundary conditions takes effect along the non-axis plane of the cylinder. If this parameter is defined, then cylindricalBCl2 and spericalBCk2 must also be defined.

• cylindricalBCl2 radius for second boundary condition (Å)
Acceptable Values: positive decimal
Description: Distance at which the second potential of the boundary conditions takes effect along the cylinder axis. If this parameter is defined, then cylindricalBCr2 and spericalBCk2 must also be defined.

• cylindricalBCk2 force constant for second potential
Acceptable Values: non-zero decimal
Description: Force constant for the second harmonic potential. A positive value will push atoms toward the center, and a negative value will pull atoms away from the center.

• cylindricalBCexp2 exponent for second potential
Acceptable Values: positive, even integer
Default Value: 2
Description: Exponent for second boundary potential. The only likely values to use are 2 and 4.

### Periodic boundary conditions

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

• cellBasisVector1 basis vector for periodic boundaries (Å)
Acceptable Values: vector
Default Value: 0 0 0
Description: Specifies a basis vector for periodic boundary conditions.

• cellBasisVector2 basis vector for periodic boundaries (Å)
Acceptable Values: vector
Default Value: 0 0 0
Description: Specifies a basis vector for periodic boundary conditions.

• cellBasisVector3 basis vector for periodic boundaries (Å)
Acceptable Values: vector
Default Value: 0 0 0
Description: Specifies a basis vector for periodic boundary conditions.

• cellOrigin center of periodic cell (Å)
Acceptable Values: position
Default Value: 0 0 0
Description: When position rescaling is used to control pressure, this location will remain constant. Also used as the center of the cell for wrapped output coordinates.

• extendedSystem XSC file to read cell parameters from
Acceptable Values: file name
Description: In addition to .coor and .vel output files, NAMD generates a .xsc (eXtended System Configuration) file which contains the periodic cell parameters and extended system variables, such as the strain rate in constant pressure simulations. Periodic cell parameters will be read from this file if this option is present, ignoring the above parameters.

• XSTfile XST file to write cell trajectory to
Acceptable Values: file name
Description: NAMD can also generate a .xst (eXtended System Trajectory) file which contains a record of the periodic cell parameters and extended system variables during the simulation. If XSTfile is defined, then XSTfreq must also be defined.

• XSTfreq how often to append state to XST file
Acceptable Values: positive integer
Description: Like the DCDfreq option, controls how often the extended system configuration will be appended to the XST file.

• wrapWater wrap water coordinates around periodic boundaries?
Acceptable Values: on or off
Default Value: off
Description: Coordinates are normally output relative to the way they were read in. Hence, if part of a molecule crosses a periodic boundary it is not translated to the other side of the cell. This option alters this behavior for water molecules only.

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