Next: Energy Minimization
Up: Standard Minimization and Dynamics
Previous: Standard Minimization and Dynamics
Subsections
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. 8.11.
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
Default Value: outputname.xst
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.
- wrapAll
wrap all 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 on output. This option applies a translation to the center-of-mass of each molecule or contiguous cluster of bonded atoms to keep it within the periodic unit cell.
The translation has usually no effect on the physical trajectory, because the force field potentials used in NAMD follow the minimum-image convention for interatomic distances. However, some complex quantities, for example the center of mass of a multimeric protein, will be undefined as a result of this option.
If you plan on applying external forces (SMD, tclForces or Colvars) to such quantities, it is recommended to keep this option off, and to possibly replace it with a custom restraint.
- wrapWater
wrap water coordinates around periodic boundaries?
Acceptable Values: on or off
Default Value: off
Description: This option is similar to the wrapAll option, but its effect is restricted to water molecules only.
- wrapNearest
use nearest image to cell origin when wrapping coordinates?
Acceptable Values: on or off
Default Value: off
Description: Coordinates are normally wrapped to the diagonal unit cell centered on the origin. This option, combined with wrapWater or wrapAll, wraps coordinates to the nearest image to the origin, providing hexagonal or other cell shapes.
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.
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.
Next: Energy Minimization
Up: Standard Minimization and Dynamics
Previous: Standard Minimization and Dynamics
http://www.ks.uiuc.edu/Research/namd/