Note
This website is presently under development. The primary website for MOPAC is still http://openmopac.net until the majority of its contents have been migrated here.
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 <gnorm.html>`__=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:
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 |
See also `OPT("Label"=n.nn) <opt_label.html>`__