6.5. Semi-Empirical QM ‣ MOPAC menu

It is a menu related to MOPAC.

MOPAC 6 and MOPAC 7 are bundled with Winmostar. When using other MOPAC please purchase MOPAC body separately from distributor and set the path in Preferences window.

6.5.1. Configure

Set calculation condition of MOPAC. To set up the calculations immediately after setting Run button, once to return to the main window please press OK button.

Behavior when clicking Run is see (1) Run MOP6W70, (2) Run MOP7W70, (3) Run MOPACX.

return to the default state with Reset button. . Save the current state as the default state with Save as Default button. Restore the default state to the factory condition with Save as Default ‣ Clear Default Settings.

Easy Setup
The simple setting window is displayed.

Specify the Hamiltonian to use. The Hamiltonian supported by each version of MOPAC is as follows.

Hamiltonian Version of MOPAC being implemented
AM1 MOPAC 6, MOPAC 7, MOPAC 93, MOPAC 97, MOPAC 2000, MOPAC 2002, MOPAC 2006, MOPAC 2009, MOPAC 2012
PM3 MOPAC 6, MOPAC 7, MOPAC 93, MOPAC 97, MOPAC 2000, MOPAC 2002, MOPAC 2006, MOPAC 2009, MOPAC 2012
RM1 MOPAC 2007
AM1 EXTERNAL=RM1.rm1 MOPAC 7.1, MOPAC 93, MOPAC 97, MOPAC 2000, MOPAC 2002, MOPAC 2006, MOPAC 2009, MOPAC 2012
PM5 MOPAC 2002, MOPAC 2006
PM6 MOPAC 2007, MOPAC 2009, MOPAC 2012
PM7 MOPAC 2012
MINDO/3 MOPAC 6, MOPAC 7, MOPAC 93, MOPAC 97, MOPAC 2000, MOPAC 2002, MOPAC 2006
MNDO MOPAC 6, MOPAC 7, MOPAC 93, MOPAC 97, MOPAC 2000, MOPAC 2002, MOPAC 2006, MOPAC 2009, MOPAC 2012
MNDO-d MOPAC 97, MOPAC 2000, MOPAC 2002, MOPAC 2006, MOPAC 2009, MOPAC 2012

Specify the calculation method.

Perform structure optimization calculation by EF (Eigen Vector Following) method.
Find the transition state.
Perform vibration analysis.
Perform SCF calculation only once. (Structure optimization is not performed.)
Perform unique reaction coordinate calculation. Energy is not preserved.
Specify the inverse direction of the 1st reference vibration and calculate the unique reaction coordinate.
Specify the positive direction of the first reference vibration and perform the unique reaction coordinate calculation.
Specify the value of the charge.
Specify multiplicity.
Specify the number of electrons and the number of orbits in open shell calculation.
Molecular dynamics correction is added to CONH bond.
Molecular mechanics correction is not added to CONH bond.
Specify the threshold value of the energy gradient norm.
Information is output for each specified cycle.
Create a file to graphically display molecular orbitals. (GPAGH/GRAPHF)
Read parameter file on disk.
Specify the step width in reaction coordinate calculation.
Specify the number of calculation points in reaction coordinate calculation.
Specify the step size in the grid calculation.
Specify the number of calculation points in the grid calculation.
Create an AUX file for use with another program.
It outputs the final bond order matrix.
Specify the energy split that resolves the energy into 1 center and 2 center terms.
Calculate electrostatic potential.
Optimize the singlet first excited state.
Ignore the check if the atom is close to abnormal.
Interatomic distance is not output.
We use the same reference physical quantity value as the old version MOPAC.
Calculate the polarizability.
Set the convergence judgment condition to 100 times stricter.
Define the structure using symmetry and equivalent conditions.
Perform unrestricted Hartree-Fock calculation.
The final eigenvector (wave function) is output.
Calculation is performed using the XYZ coordinate system.
Fill in other keywords.

6.5.2. Import Keywords

Only keywords (calculation conditions) are read from the existing MOPAC input file.

6.5.3. (1) Run MOP6W70, (2) Run MOP7W70, (3) Run MOPACX

If MOPAC input file is opened in the main window, execute MOPAC using that file. If it is not open, save the input file of MOPAC and execute MOPAC.

When saving the input file, the output format of coordinates changes according to the choice of Coordinate Format ( Z-Matrix or XYZ ) and Coordinate Viewer of Z-Matrix / XYZ tab.

Difference of Run (1) MOP6W70, Run (2) MOP7W70, Run (3) MOPACX is the program path to start MOPAC. You can change the program path with Tools ‣ Preferences ‣ Program Path. Default setting MOP 6W 70 is MOPAC 6, MOP 7 W 70 is MOPAC 7, both of which are built in Winmostar. Run (3) MOPACX is assumed to be used by specifying a program such as MOPAC 2012.

Following file will be generated with execution. For example, the file/folder name when the input file is water.dat is shown together.

type Description
out file
It summarizes the outline of the calculation result.
arc file
It is a file summarizing the details of the calculation result.
mgf file
In the file outputted by specifying the keyword GRAPH,
Contains information used to draw molecular orbits.
Working Directory
Working directory.

6.5.4. Open Log File (out)

Open out file in a text editor.

6.5.5. Open Log File (arc)

Open arc file with a text editor.

6.5.6. Animation Optimization (arc)

Select the arc file and display the animation of the molecular structure.

For the animation display operation method, see Animation window. IRC, STEP (out)

Select out file and display animation of IRC calculation.

For the animation display operation method, see Animation window.

6.5.7. Analyses MO & Density (mgf)

Select the mgf file and display the molecular orbital.

GRAPHF must be set on keyword. Refer to Energy Level Diagram window, MO Plot window for how to operate the subwindow. Charges (arc)

Select arc file and display charge, dipole.

Show charges when you select View ‣ Label/Charges ‣ Show Mulliken Charge. IR (out)

Select the out file and display the IR spectrum.

Vibration calculation must be set with keyword. Refer to IR Spectrum Window for how to operate the subwindow.

6.5.8. Use Job Manager

When checked, use Winmostar Job Manager when executing MOPAC. Otherwise, Winmostar will be in a wait state until calculation by MOPAC is completed, and the output result of MOPAC will be automatically loaded into the main window.

It can also be set from Tools ‣ Preferences menu.