Harmonic constraints

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. For further details, see section 5.1.8.

• constraints $\langle$ Are constraints active? $\rangle$
  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 $\langle$ exponent for harmonic constraint energy function $\rangle$
  Acceptable Values: positive, even integer
  Default Value: 2
  Description: Exponent to be used 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 $\langle$ PDB file containing constraint reference positions $\rangle$
  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 to 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 to their initial positions.

• conskfile $\langle$ PDB file containing force constant values $\rangle$
  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 $\langle$ column of PDB file containing force constant $\rangle$
  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 (in kcal/mol/Ų). NOTE: NAMD actually calculates the constraints potential with U = k (x-x₀)^d and the force with F = -d k (x-x₀)^d-1, where d is the exponent consexp. This means that for the force constant k given in the PDB file, the actual force constant is d k in calculations.