Constraints and Restraints

Harmonic constraint parameters

The following describes the parameters for the harmonic constraints feature of NAMD. Actually, this feature should be referred to as harmonic restraints rather than constraints, but for historical reasons the terminology of harmonic constraints has been carried over from X-PLOR. This feature allows a harmonic restraining force to be applied to any set of atoms in the simulation.

• constraints $<$ are constraints active? $>$
  Acceptable Values: on or off
  Default Value: off
  Description: Specifies whether or not harmonic constraints are active. If it is set to off, then no harmonic constraints are computed. If it is set to on, then harmonic constraints are calculated using the values specified by the parameters consref, conskfile, conskcol, and consexp.

• consexp $<$ exponent for harmonic constraint energy function $>$
  Acceptable Values: positive, even integer
  Default Value: 2
  Description: Exponent to be use in the harmonic constraint energy function. This value must be a positive integer, and only even values really make sense. This parameter is used only if constraints is set to on.

• consref $<$ PDB file containing constraint reference positions $>$
  Acceptable Values: UNIX file name
  Default Value: coordinates
  Description: PDB file to use for reference positions for harmonic constraints. Each atom that has an active constraint will be constrained about the position specified in this file. If no value is given and constraints are active, then the same PDB file specified by coordinates will be used instead, constraining atoms about their initial positions.

• conskfile $<$ PDB file containing force constant values $>$
  Acceptable Values: UNIX filename
  Default Value: coordinates
  Description: PDB file to use for force constants for harmonic constraints. If this parameter is not specified, then the PDB file containing initial coordinates specified by coordinates is used.

• conskcol $<$ column of PDB file containing force constant $>$
  Acceptable Values: X, Y, Z, O, or B
  Default Value: O
  Description: Column of the PDB file to use for the harmonic constraint force constant. This parameter may specify any of the floating point fields of the PDB file, either X, Y, Z, occupancy, or beta-coupling (temperature-coupling). Regardless of which column is used, a value of 0 indicates that the atom should not be constrained. Otherwise, the value specified is used as the force constant for that atom's restraining potential.

• selectConstraints $<$ Restrain only selected Cartesian components of the coordinates? $>$
  Acceptable Values: on or off
  Default Value: off
  Description: This option is useful to restrain the positions of atoms to a plane or a line in space. If active, this option will ensure that only selected Cartesian components of the coordinates are restrained. E.g.: Restraining the positions of atoms to their current z values with no restraints in x and y will allow the atoms to move in the x-y plane while retaining their original z-coordinate. Restraining the x and y values will lead to free motion only along the z coordinate.

• selectConstrX $<$ Restrain X components of coordinates $>$
  Acceptable Values: on or off
  Default Value: off
  Description: Restrain the Cartesian x components of the positions.
• selectConstrY $<$ Restrain Y components of coordinates $>$
  Acceptable Values: on or off
  Default Value: off
  Description: Restrain the Cartesian y components of the positions.
• selectConstrZ $<$ Restrain Z components of coordinates $>$
  Acceptable Values: on or off
  Default Value: off
  Description: Restrain the Cartesian z components of the positions.

Fixed atoms parameters

Atoms may be held fixed during a simulation. NAMD avoids calculating most interactions in which all affected atoms are fixed.

• fixedAtoms $<$ are there fixed atoms? $>$
  Acceptable Values: on or off
  Default Value: off
  Description: Specifies whether or not fixed atoms are present.

• fixedAtomsFile $<$ PDB file containing fixed atom parameters $>$
  Acceptable Values: UNIX filename
  Default Value: coordinates
  Description: PDB file to use for the fixed atom flags for each atom. If this parameter is not specified, then the PDB file specified by coordinates is used.

• fixedAtomsCol $<$ column of PDB containing fixed atom parameters $>$
  Acceptable Values: X, Y, Z, O, or B
  Default Value: O
  Description: Column of the PDB file to use for the containing fixed atom parameters for each atom. The coefficients can be read from any floating point column of the PDB file. A value of 0 indicates that the atom is not fixed.