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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 as described in the NAMD Programmer's Guide. 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 sphericalBCr1 and sphericalBCk1 must be defined, and sphericalBCexp1, sphericalBCr2, sphericalBCk2, and sphericalBCexp2 can optionally be defined.

• 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 of mass.

• 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 of mass, and a negative value will pull atoms away from the center of mass.

• 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 of mass. 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 of mass, and a negative value will pull atoms away from the center of mass.

• 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 as described in the NAMD Programmer's Guide. 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 cylindricalBCr1, cylindricalBCl1 and cylindricalBCk1 must be defined, and cylindricalBCAxis, cylindricalBCCenter, 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. If not specified, center of mass is used.

• 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 basis vectors of the periodic cell must be along the x, y, and z axes. This restriction will be eliminated in future versions of NAMD. The following parameters are used to define these boundary conditions.

• cellBasisVector1 < basis vector for periodic boundaries (Å) >
Acceptable Values: vector along x axis
Default Value: 0 0 0
Description: Specifies whether or not periodic boundary conditions are to be applied to the system in the x direction.

• cellBasisVector2 < basis vector for periodic boundaries (Å) >
Acceptable Values: vector along y axis
Default Value: 0 0 0
Description: Specifies whether or not periodic boundary conditions are to be applied to the system in the y direction.

• cellBasisVector3 < basis vector for periodic boundaries (Å) >
Acceptable Values: vector along z axis
Default Value: 0 0 0
Description: Specifies whether or not periodic boundary conditions are to be applied to the system in the z direction.

• 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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