6.5. QM ‣ MOPAC menu

It is a menu related to MOPAC.

MOPAC6 and MOPAC7 are bundled with Winmostar. If you wish to use other MOPACs, please obtain the MOPAC itself separately and set the path in the Preferences window.

6.5.1. Workflow Setting

Set up and run MOPAC calculation flow in project mode.

Preset

Loads and saves a preset of settings.

# of Jobs

Specifies the number of jobs.

Enable scan calculation

This feature requires the purchase of an add-on. It allows you to run multiple calculations where only certain parameters differ (parameter scan) or to run calculations with the same parameters for multiple structures (structure scan).

Click Config to open the configuration window for the scan calculation. For parameter scans, select %WM_SCAN1% for the Target Variable and enter the parameters you wish to set for %WM_SCAN1% in each row of the Values. Then, enter %WM_SCAN1% in the parameters you want to set in the Workflow Settings window or Keyword Settings window. For structure scan, select %WM_STRUCT% for Target Variable when the animation appears in the molecule display area (e.g., by opening an SDF file).

After the scan calculation is finished, use File ‣ Project ‣ Scan Results to tabulate the calculation results.

Import

Import the settings output by Export. Click the arrow to the right of the button to recall settings used in the past on the same project or Winmostar.

Export

Output settings to file.

OK

Run a calculation or generate a file with your settings.

Details

Set up detailed calculation conditions. The Configure will be launched.

Task

Specifies the type of calculation.


Configuration details
Energy
Method=1SCF
Optimize
Method=EF
IR
Method=FORCE
Optimize(TS)
Method=TS
IRC(Forward)
Method=IRC=1
LARGE=50
IRC(Reverse)
Method=IRC=-1
LARGE=50
Scan
Method=EF
Add the specified Scan content to the last line of input.
Method

Specify the calculation method (Hamiltonian).

UHF

Specify whether the calculation should be done in a closed or open shell system.

Charge

Specify charge.

Multiplicity

Specifies spin multiplicity.

6.5.2. 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.

Hamiltonian

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

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

Method

Specify the calculation method.

EF

Perform structure optimization calculation by EF (Eigen Vector Following) method.

TS

Find the transition state.

FORCE

Perform vibration analysis.

1SCF

Perform SCF calculation only once. (Structure optimization is not performed.)

IRC

Perform unique reaction coordinate calculation. Energy is not preserved.

IRC=1

Specify the inverse direction of the 1st reference vibration and calculate the unique reaction coordinate.

IRC=-1

Specify the positive direction of the first reference vibration and perform the unique reaction coordinate calculation.

Charge

Specify the value of the charge.

Multiplicity

Specify multiplicity.

OPEN

Specify the number of electrons and the number of orbits in open shell calculation.

MM
MMOK

Molecular dynamics correction is added to CONH bond.

NOMM

Molecular mechanics correction is not added to CONH bond.

GNORM

Specify the threshold value of the energy gradient norm.

LARGE

Information is output for each specified cycle.

GRAPH

Create a file to graphically display molecular orbitals. (GPAGH/GRAPHF)

EXTERNAL

Read parameter file on disk.

STEP

Specify the step width in reaction coordinate calculation.

POINT

Specify the number of calculation points in reaction coordinate calculation.

STEP1/2

Specify the step size in the grid calculation.

POINT1/2

Specify the number of calculation points in the grid calculation.

AUX

Create an AUX file for use with another program.

BONDS

It outputs the final bond order matrix.

ENPART

Specify the energy split that resolves the energy into 1 center and 2 center terms.

ESP

Calculate electrostatic potential.

EXCITED

Optimize the singlet first excited state.

GEO-OK

Ignore the check if the atom is close to abnormal.

NOINTER

Interatomic distance is not output.

OLDFPC

We use the same reference physical quantity value as the old version MOPAC.

POLAR

Calculate the polarizability.

PRECISE

Set the convergence judgment condition to 100 times stricter.

SYMMETRY

Define the structure using symmetry and equivalent conditions.

UHF

Perform unrestricted Hartree-Fock calculation.

VECTORS

The final eigenvector (wave function) is output.

XYZ

Calculation is performed using the XYZ coordinate system.

Others

Fill in other keywords.

Coordinate format

Specifies the format of the atomic coordinates (XYZ or Z-matrix).

Reset

Reset settings.

Import

Loading configuration file.

Export

Output configuration file.

6.5.3. Import Keywords

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

6.5.4. (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
water.out

It summarizes the outline of the calculation result.

arc file
water.arc

It is a file summarizing the details of the calculation result.

mgf file
water.mgf
This file is output by specifying the keyword GRAPH and contains information used to draw molecular orbitals.
Working Folder
water_mop_temp\
Working folder.

6.5.5. Open Log File (out)

Open out file in a text editor.

6.5.6. Open Log File (arc)

Open arc file with a text editor.

6.5.7. Animation

6.5.7.1. Optimization (arc)

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

For the animation display operation method, see Animation display area.

6.5.7.2. IRC, STEP (out)

Select out file and display animation of IRC calculation.

For the animation display operation method, see Animation display area.

6.5.8. Analyses

6.5.8.1. MO & Charges (mgf)

Select the mgf file and display the molecular orbital.

GRAPHF must be set on keyword. Refer to Energy Level Diagram window, Surface Setup window for how to operate the subwindow.

Show charges when you select View ‣ Label/Charges ‣ Show Mulliken Charge.

6.5.8.2. 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.

6.5.9. 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.