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.
CUTOFF¶
`MOZYME <mozyme.html>`__ calculations run faster when some NDDO
interactions are ignored. By default, all NDDO interactions are
included between atoms separated by 9.9 Ångstroms or less, and all
polarization functions between atoms separated by 10 Ångstroms or
less. For rough work, such as optimizing a structure that is far from
a minimum, if CUTOFF=n.nn is used, then only point charge
interactions beyond n.nn Ångstroms are used. A suitable value for
n.nn is 6.0. This will give a large increase in speed.CUTOFF to increase speed, first try using
CUTOFP.If CUTOFF=6 is used, then GNORM=20 is recommended. Once the
geometry is optimized using GNORM=20, the CUTOFF should be
removed, and GNORM reduced to, e.g., GNORM=10.
The effect of CUTOFF on times and accuracy of prediction of geometry
can be investigated by examining the statistics for the optimization of
the positions of hydrogen atoms in Crambin, a small 642 atom, 46 residue
protein with formula
C202H315N55O64S6,
see Table I. For a larger system, hexokinase, 2E2O, a medium-sized
protein of 5717 atoms and 299 residues,
C1448H3073N375O810S11,
results for a 1SCF calculation are shown in Table II. Hexokinase
contains 375 molecules of water.
Table I: Crambin
Table II: Hexokinase
Cutoff
Time (s)
Ratio
Distortion (Å)
Distortion (Å)
Energy (Kcal/mol)
Cutoff
Time (s)
Ratio
Energy (Kcal/mol)
Default
1328
1.00
49.5
0.0
-3342.2
0.0
Default
774
-45095.0
0.0
7.0
746
0.56
50.0
1.7
-3342.5
-0.3
12.0
796
-45095.0
0.0
6.0
889
0.76
49.6
1.3
-3342.1
+0.1
11.0
746
-45095.1
-0.1
5.0
599
0.45
46.3
8.8
-3334.5
+7.7
10.0
685
-45095.1
-0.1
4.0
348
0.26
51.7
5.0
-3315.8
+26.4
9.0
599
-45095.2
-0.2
3.0
119
0.09
34.9
26.7
-2952.1
+390.1
8.0
546
-45095.6
-0.4
no-opt
0.0
49.5
-2963.6
N/A
7.0
490
-45096.7
-1.7
6.0
343
-45093.3
+1.7
5.0
309
-50783.8
-5688.8
4.0
252
-44949.3
+145.7
For the rare occasions when finer control is needed, use CUTOF1 and
CUTOF2.
CUTOF1=n.nn¶
In MOZYME calculations, the cutoff distance for polarization
functions is set by CUTOF1=n.nn. Beyond
that distance, electrostatic interactions are considered only as point
charges. At distances less than that given by CUTOF1, electrostatic
interactions are represented by a point-charge and three polarization
functions. Default: For systems of less than 30 atoms, CUTOF1 is
1000 Ångstroms; for systems of 30 or more atoms, CUTOF1 is 10
Ångstroms.
CUTOF2=n.nn¶
In MOZYME calculations, the cutoff distance for two-electron two
center and one-electron two center integrals
is set by CUTOF2=n.nn. Below that distance, the interaction between
two atoms is represented by the exact NDDO approximation. Above that
distance, one-electron integrals that depend on the overlap are ignored,
and two-electron integrals are simplified. Instead of using all 100
two-electron integrals between two heavy atoms, only seven are used.
These represent the terms <ss|ss>, <ss|sx>,
<ss|sy>, <ss|sz>, <sx|ss>, <sy|ss>,
and <sz|ss>. At still greater distances, beyond CUTOF1,
only the <ss|ss> term is used. Default: for systems of less
than 30 atoms, CUTOF2 is 1000 Ångstroms; for systems of 30 or more
atoms, CUTOF2 is 9.9 Ångstroms.