How to Run MOPAC Commands (with Examples)

MOPAC, short for Molecular Orbital PACkage, is a semiempirical quantum chemistry program developed to facilitate the modeling and simulation of molecular structures and reactions. Based on the NDDO (Neglect of Diatomic Differential Overlap) approximation by Dewar and Thiel, MOPAC allows users to perform a wide array of quantum chemistry computations with simplicity and efficiency. It supports various types of calculations, making it a versatile tool for researchers and scientists in the field of chemistry.

Use Case 1: Perform Calculations According to an Input File

Code:

mopac path/to/input_file

Motivation:

Chemical researchers often deal with complex molecular systems that require precise calculations of chemical properties, such as enthalpy, charge distribution, and geometries. To facilitate these computations, MOPAC allows users to provide input data through specific file formats like .mop, .dat, or .arc. Applying these input files in a calculation ensures that all necessary parameters are prepared and integrated into the simulation environment.

Explanation:

• mopac: This is the command that invokes the MOPAC program.
• path/to/input_file: This is a placeholder for the actual path of the input file. The file path should refer to a valid MOPAC input file that contains the required details for the calculation.

Example Output:

When executing the command with a specified input file, MOPAC processes the file to perform the associated chemical calculations. Upon completion, the output typically includes computational results such as energy levels, optimized geometries, and electronic distribution, formatted in a systematic report that can be reviewed for further research and analysis.

Use Case 2: Minimal Working Example with HF

Code:

touch test.out; echo "PM7\n#comment\n\nH 0.95506 0.05781 -0.03133\nF 1.89426 0.05781 -0.03133" > test.mop; mopac test.mop & tail -f test.out

Motivation:

Suppose a researcher wants to perform a quick and simple calculation on a small molecular system without complex configurations. In this example, we focus on the hydrogen fluoride (HF) molecule, showcasing a minimal input setup using MOPAC’s PM7 method. This approach is beneficial for testing configurations, preparing educational demonstrations, and validating hypotheses before scaling to more sophisticated systems.

Explanation:

• touch test.out: Creates an empty file called test.out that will be used to stream MOPAC’s output.
• echo "PM7\n#comment\n\nH 0.95506 0.05781 -0.03133\nF 1.89426 0.05781 -0.03133" > test.mop: This command writes the PM7 calculation method and molecular coordinates of HF into a file named test.mop. The coordinates specify the spatial arrangement of hydrogen (H) and fluorine (F) atoms.
• mopac test.mop: Executes MOPAC using test.mop as the input file, beginning the calculation based on the specified configuration.
• &: Places the MOPAC process in the background, allowing subsequent commands to run simultaneously.
• tail -f test.out: Continuously displays the contents of test.out, providing a real-time live stream of MOPAC’s output as the calculation progresses.

Example Output:

Executing this command initiates the calculation of the HF molecule’s properties using the PM7 method. The output, streamed via test.out, contains the ongoing computational details, such as iterations of energy minimization, changes in atomic positions, expected dipole moments, and final energy status of the system under consideration.

Conclusion:

Utilizing MOPAC efficiently requires a thorough understanding of input formatting and command structuring, as illustrated by the above examples. These use cases demonstrate MOPAC’s ability to handle varying complexity levels in quantum chemical calculations, providing insightful data across both simple and elaborate scenarios. Whether for energy predictions, molecular geometry optimizations, or validating theoretical models, MOPAC stands as a powerful tool indispensable to the realm of chemistry research.