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11.1 Restraining Atomic Movements

11.1.1 Syntax of Harmonic Atom Constraints

     CONStraint HARMonic FORCE real [PRINT] [REF coor-spec del]
                [MASS] atom-selection

coor-spec is a specification for the coordinates. See Read Syntax, for the syntax.

Syntactic ordering: HARMonic must follow CONStraint, and FORCE must follow HARMonic.

11.1.2 Function of Harmonic Atom Constraints

The potential energy has a harmonic constraint term which allows one to prevent large motions of individual atoms. The form for this potential is as follows for coordinates:

EC = sum over all atoms of k(i)/2 * (x(i)-refx(i))**2

where refx is a reference set of coordinates. If MASS is specified in the command line, then k is multiplied by the mass of the atom resulting in a natural frequency of oscillation for the constraint of sqrt(k) in AKMA units. An atom constrained with MASS FORCE 1.0 will oscillate at 7.6 cycles/picosecond if free of other interactions.

CONGEN supports a number of operations on the coordinate constraints. The constraint for any atom can be set to any positive value (specified by the FORCE keyword followed by the desired value). The reference coordinates can be the current set at the point when constraints are specified (the default) or a set can be read from a coordinate file (specified by REF and a coor-spec). The force constants and reference coordinates can read or written as a unit. The PRINT option prints a list of all the current harmonic constraints that are applied to the system after this command has been executed.

It is important to understand some aspects of how the constraints are set in order to get the most flexibility out of this command. When CONGEN is loaded, each atom has associated with it a harmonic force constant initially set to zero. Each call to the CONSTRAINT HARMONIC command changes the value of this constant for only those atoms specified.

11.1.3 Other Commands for Harmonic Atom Constraints

The harmonic constraints may be read and written to files. The file name to be specified in the READ and WRITE command is CONS. The files may be read or written only in binary. The PRINT command will also work for constraints. See I/O, for more details. In addition, one may look at the contributions to the energy in detail using the analysis facility, see Analysis.

PRINT specifies that a listing of of all the atoms currently constrained should be printed out. This is done by segments of constrained atoms, which is concise in most cases. Unfortunately in the case of IUPAC specified constraints it is quite verbose.