MINI

When very large molecules such as enzymes are modeled, the output can become very large.  To reduce this, use MINI.  When MINI is present, only atoms whose coordinates are flagged with a "2" will be printed.  During a run, atoms flagged with a "2" will be handled as if they were flagged with a "1".  That is, the flag "2" will indicate an atom that is marked for optimization. For reaction paths, the reaction coordinate is normally "-1", if  MINI is present then the reaction coordinate can be "-1" or "-2" ("-2" is obviously more likely). Although MINI works with all types of calculation, the main use would be for calculations that involve reaction paths and IRC paths. 

MINI is also useful when animations are involved, for example mapping out a reaction path or following an IRC or DRC.   If HTML is present, then a HTML document will be created that can be run using Firefox.  If GRAPHF is present in runs that produce animations then a file, <file>.xyz, will be generated.  This can be visualized using Jmol.

When MINI and TS are both present, a transition state optimization calculation is run, and only atoms that are flagged with the symbol "2" will be printed; their positions will be changed during the optimization run. All nearby atoms that are to be moved during the optimization should be flagged with a "1", these atoms will not be printed.  More distant atoms should be flagged with "0" to indicate that their positions are fixed (frozen); they will not be printed.

MINI and FORCETS can be used with internal or Cartesian coordinates.  There are two ways to run MINI - FORCETS jobs:

(A) Running MINI and FORCETS in one job; this is not recommended for large systems. Use keywords HTML FORCETS IRC MINI  plus others, to suit.  Set optimization flags to "2" for the atoms to be used in FORCETS, and to "0" for all other atoms. 

(B) Running MINI and FORCETS in two jobs; this is the recommended method for large systems.  In the first job, use keywords FORCETS ISOTOPE plus any others needed.  Set optimization flags to "1" for the atoms to be used in FORCETS, and to "0" for all other atoms.  In a second job, use keywords HTML FORCETS IRC MINI RESTART plus others to suit. Use the same geometry plus flags as in the first job.  To add an atom to the set of atoms printed, change its optimization flags from "0" to "2".  This gives increased flexibility in that the atoms used in the FORCETS calculation need to be as few as possible, because the FORCETS calculation is CPU intensive, but increasing the number of atoms printed in the IRC calculation only affects the files generated.

When MINI and 0SCF are both present then a file, <file>.xyz, will be generated.

MINI is useful when locating transition states, in FORCETS calculations, in following reaction paths, and in IRC and DRC trajectories.

If PDBOUT is present, a PDB file will also be written; this file will be complete.  So if a complete geometry is wanted, as well as the minimized geometry, then add PDBOUT

: Re-written August 2016