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11.4 Fixing Atoms in Place

11.4.1 Syntax for Fixing Atoms

     CONS FIX atom-selection-spec [PURG] [BOND] [THET] [PHI] [IMPH]

11.4.2 Function of Fixing Atoms

This command fixes atoms in place by setting flags in an array (IMOVE) which tells the minimization and dynamics algorithms which atoms are free to move. If atoms are fixed, it is possible to save computer time by not calculating energy terms which involve only fixed atoms. The nonbond and hydrogen bond algorithms in CONGEN check IMOVE and delete pairs of atoms that are fixed in place from the nbond and hbond lists respectively. In addition the PURG or individual energy term options specified with the CONS FIX command allow all or some of the internal coordinate energies associated with fixed atoms to be deleted. Interactions between fixed and moving atoms are maintained.

N.B. Because some energy terms are deleted from fixed systems, the total energy calculated with fixed atoms will be different from the total energy of the same system with all atoms free. The forces on the moveable atoms will however be identical.

The way CONGEN keeps track of fixed atoms is by the IMOVE array in the PSF. The IMOVE array is 0 if the atom is free to move, and has some other value if the atom is fixed. WARNING: the use of IMOVE is not yet universal in CONGEN. At present (November 15, 1990), it is supported for dynamics, all forms of minimization except Newton-Raphson. The vibrational analysis does not yet support it.

NOTE: If you use SHAKE in conjunction with fixed atoms, you should specify the SHAKE command after you have specified the fixed atoms. This will prevent SHAKE from compiling a list of bonds from which the CONS command will delete after it has a list of fixed atoms.

If PURGE is specified, every bond, bond angle, torsion angle, or improper torsion involving only fixed atoms is deleted. One can limit this elimination process to one type of interaction by specifying BOND, ANGL, PHI, or IMPH. By playing games with combinations of these commands, one can eliminate whole terms from the energy expression.