Constraints and Restraints

Bond constraint parameters

• rigidBonds $<$ controls if and how ShakeH is used $>$
  Acceptable Values: none, water, all
  Default Value: none
  Description: When water is selected, the hydrogen-oxygen and hydrogen-hydrogen distances in waters are constrained to the nominal length or angle given in the parameter file, making the molecules completely rigid. When rigidBonds is all, waters are made rigid as described above and the bond between each hydrogen and the (one) atom to which it is bonded is similarly constrained. For the default case none, no lengths are constrained.

• rigidTolerance $<$ allowable bond-length error for ShakeH (Å) $>$
  Acceptable Values: positive decimal
  Default Value: 1.0e-8
  Description: The ShakeH algorithm is assumed to have converged when all constrained bonds differ from the nominal bond length by less than this amount.

• rigidIterations $<$ maximum ShakeH iterations $>$
  Acceptable Values: positive integer
  Default Value: 100
  Description: The maximum number of iterations ShakeH will perform before giving up on constraining the bond lengths. If the bond lengths do not converge, a warning message is printed, and the atoms are left at the final value achieved by ShakeH. Although the default value is 100, convergence is usually reached after fewer than 10 iterations.

• rigidDieOnError $<$ maximum ShakeH iterations $>$
  Acceptable Values: on or off
  Default Value: on
  Description: Exit and report an error if rigidTolerance is not achieved after rigidIterations.

• useSettle $<$ Use SETTLE for waters. $>$
  Acceptable Values: on or off
  Default Value: on
  Description: If rigidBonds are enabled then use the non-iterative SETTLE algorithm to keep waters rigid rather than the slower SHAKE algorithm.

Position restraint parameters

The following describes the parameters for the position restraints feature of NAMD. For historical reasons the term ``constraints'' has been carried over from X-PLOR. This feature allows a restraining potential to each atom of an arbitrary set during the simulation.

• constraints $<$ are position restraints active? $>$
  Acceptable Values: on or off
  Default Value: off
  Description: Specifies whether or not position restraints are active. If it is set to off, then no position restraints are computed. If it is set to on, the potential $k\times(\mathbf{x} - \mathbf{x}_0)^p$ is applied to each atom. Per-atom values for $k$ can be defined by either conskfile or conskcol, for $\mathbf{x}_0$ by consref, and for $p$ by consexp.

• consexp $<$ exponent for position restraint energy function $>$
  Acceptable Values: positive, even integer
  Default Value: 2
  Description: Exponent to be use in the position restraint 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 restraint reference positions $>$
  Acceptable Values: UNIX file name
  Description: PDB file to use for reference positions for position restraints. Each atom that has a positive force constant will be restrained about the position specified in this file.

• conskfile $<$ PDB file containing force constant values $>$
  Acceptable Values: UNIX filename
  Description: PDB file to use for force constants for position restraints.

• conskcol $<$ column of PDB file containing force constant $>$
  Acceptable Values: X, Y, Z, O, or B
  Description: Column of the PDB file to use for the position restraint 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 qshould not be restrained. Otherwise, the value specified is used as the force constant for that atom's restraining potential.

• constraintScaling $<$ scaling factor for position restraint energy function $>$
  Acceptable Values: positive
  Default Value: 1.0
  Description: The position restraint energy function is multiplied by this parameter, making it possible to gradually turn off restraints during equilibration. This parameter is used only if constraints is set to on.

• 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 unless fixedAtomsForces is specified.

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

• fixedAtomsForces $<$ are forces between fixed atoms calculated? $>$
  Acceptable Values: on or off
  Default Value: off
  Description: Specifies whether or not forces between fixed atoms are calculated. This option is required to turn fixed atoms off in the middle of a simulation. These forces will affect the pressure calculation, and you should leave this option off when using constant pressure if the coordinates of the fixed atoms have not been minimized. The use of constant pressure with significant numbers of fixed atoms is not recommended.

• 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.

Extra bond, angle, and dihedral restraints

Additional bond, angle, and dihedral energy terms may be applied to system, allowing secondary or tertiary structure to be restrained, for example. Extra bonded terms are not considered part of the molecular structure and hence do not alter nonbonded exclusions. The energies from extra bonded terms are included with the normal bond, angle, and dihedral energies in NAMD output.

All extra bonded terms are harmonic potentials of the form $U(x) = k (x-x_{ref})^2$ except dihedrals and impropers with a non-zero periodicity specified, which use $U(x) = k (1 + cos(n x - x_{ref}))$ . The only difference between dihedrals and impropers is the output field that their potential energy is added to.

Due to a very old bug all NAMD releases prior to 2.13 have used the MARTINI cosine-based angle potential function for all extra angles. Since workflows may unknowingly depend on this undocumented behavior, cosine-based angles remain the default, but a warning is printed unless the desired behavior is specified via the new option extraBondsCosAngles (defaults to ``on'', set to ``off'' to use the normal harmonic angle potential function for all extra angles).

The extra bonded term implementation shares the parallel implementation of regular bonded terms in NAMD, allowing large numbers of extra terms to be specified with minimal impact on parallel scalability. Extra bonded terms do not have to duplicate normal bonds/angles/dihedrals, but each extra bond/angle/dihedral should only involve nearby atoms. If the atoms involved are too far apart a bad global bond count will be reported in parallel runs.

Extra bonded terms are enabled via the following options:

• extraBonds $<$ enable extra bonded terms? $>$
  Acceptable Values: on or off
  Default Value: off
  Description: Specifies whether or not extra bonded terms are present.

• extraBondsCosAngles $<$ are extra angles cosine-based? $>$
  Acceptable Values: on or off
  Default Value: on
  Description: Specifies whether or not all extra angles are cosine-based for consistency with previous versions. Set to off to use normal harmonic angle potential for all extra angles.

• extraBondsFile $<$ file containing extra bonded terms $>$
  Acceptable Values: file
  Description: File containing extra bonded terms. May be repeated for multiple files.

The extra bonds file(s) should contain lines of the following formats:

• bond <atom> <atom> <k> <ref>
• angle <atom> <atom> <atom> <k> <ref>
• dihedral <atom> <atom> <atom> <atom> <k> <ref>
• dihedral <atom> <atom> <atom> <atom> <k> <n> <ref>
• improper <atom> <atom> <atom> <atom> <k> <ref>
• improper <atom> <atom> <atom> <atom> <k> <n> <ref>
• # <comment ...>

In all cases <atom> is a zero-based atom index (the first atom has index 0), <ref> is a reference distance in Å (bond) or angle in degrees (others), and <k> is a spring constant in the potential energy function $U(x) = k (x-x_{ref})^2$ or, for dihedrals and impropers with periodicity <n> specified and not 0, $U(x) = k (1 + cos(n x - x_{ref}))$ . Note that $x_{ref}$ is only a minimum for the harmonic potential; the sinusoidal potential has minima at $(x_{ref} + 180)/n + i \times 360/n$ .