RAPID

`RAPID`

When only part of a geometry is being modified, the speed of a MOZYME SCF calculation can be increased by the use of RAPID. Thus, if a side-chain on a protein is being optimized, all atoms on the side-chain would be flagged with " 1 "s, and all other atoms would be flagged with " 0 "s. An atom is considered as being modified if any one of the three flags is " 1 ". RAPID should not be used if many atoms are to be optimized and those atoms are not all in one part of the molecule. For example, RAPID should not be used with NOOPT OPT-H.

Because of limitations in RAPID, the termination criterion should be quite large - say GNORM=5 or more. Also, after a RAPID calculation, a conventional MOZYME calculation should be run, in order to get a more correct heat of formation.

If the following conditions are used, the optimization will run smoother:

1. Use Cartesian coordinates.
2. Before using RAPID, a useful step is to optimize the whole system.

The effort to set up a system with RAPID is well worth while, particularly if only a few (up to 10-20%) of the atoms are flagged.

As an example of the effect of using RAPID, for a decapeptide containing 143 atoms, with the coordinates of the atoms of the last residue being optimized, the times required for 10 cycles of geometry optimization are as follows:

Method	Time (s)
Using conventional MOPAC	19.4
Using MOZYME	5.5
Using MOZYME with RAPID	2.8