molUP Tutorial 2 – Load a Gaussian output and prepare a scan

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On the last week, a detailed tutorial about how to start a QM/MM study using molUP was published here. That tutorial finished with the creation of a Gaussian input file. In this new tutorial, we will see how to load the Gaussian output file that resulted from the calculation. Moreover, the Gaussian output will be used to start a new calculation, in this case, a scan of a reaction coordinate.

Open a Gaussian Output file using molUP

The process could not be simpler, only requires a few steps:

  1. Launch VMD;
  2. Start molUP through the “Extensions” > “VMD Store” > “molUP” menu;
  3. On the molUP window, go to “File” > “Open”;
  4. Browse the Gaussian Output file (.log);
  5. Under the “Loading options”, choose “Last structure”;
  6. Click on “Load”.

molUP provides four loading options:

  • First structure
    This option loads the first structure available on the Gaussian output file. It means that the loaded structure will be equal to the one available on the Gaussian input file used in the calculation.
  • Last structure
    This option loads the final optimized structure available on the Gaussian output file. However, if the calculation does not finish, the last structure will be loaded, and an alert will be displayed informing about an unfinished job.
  • All optimized structures
    This option load all the optimized structures from a Gaussian output file that resulted from a scan calculation (it will be discussed later).
  • All structures
    During an optimization, several intermediate structures are generated during the Gaussian calculation. This option shows all those structures.
    WARNING The loading process could be time-consuming if the file contains a big number of structures.

NOTE The connectivity and parameters will only be loaded if the Gaussian input file used for the calculation is available in the same directory where the output file was browsed. Therefore, ensure that the Gaussian input and output files are in the same directory before loading the output file using molUP. Example:

/path/opt.com
/path/opt.log

Understanding the output

After the loading process finishes, the structure will be available to visualize, and the output section will be populated by the data available in the Gaussian output file.

In this case, the “Output” tab provides information about the total energy computed for the system (Hartree) and also the energy calculated for each ONIOM layer (High-level (HL) and Low-level (LL) layers). Additionally, there is a “i” button that provides insights about how the energy was calculated and how to interpret the energy values by ONIOM layer.

The “Output” section can also be populated with data about thermal corrections, energy profiles from scans, and vibrational frequencies analysis but these features will only be discussed in future tutorials.

Prepare a scan of a reaction coordinate

Following the workflow of this tutorial, after the initial geometry optimization, we are interested in studying a specific reaction. Therefore, a new Gaussian input file must be prepared to perform a scan of a reaction coordinate.

  1. On the molUP window, go to the “Input” section;
  2. (Optional) Change the job’s name under the “Job title” field;
  3. Adjust the calculation keywords to match your needs. In this case, it is important the ModRed option associated with the opt keyword in order to instruct Gaussian to perform a scan:
    opt=ModRed
  4. Click on “Other information (Parameters, ModRedundant…)” menu and select “ModRedundant Editor”;
  5. On the new pop-up window, click on “Pick” to select the pair of atoms involved in the reaction;
  6. Provide the number of steps that will be taken during the calculation (choose an integer number > 1);
  7. Provide the size of the step in Å. Positive numbers will increase the distance between both atoms whereas negative numbers will short their interatomic distance;
    ATTENTION Do not choose a large step’s size because it could generate geometric clashes.
  8. Click on “Apply”;
  9. On the “Other information (Parameters, ModRedundant…)” field, insert a black line before the ModRedundant information (B XXXXX XXXXX S XX X.XXX) and two blank lines between the ModRedundant information and the parameters section.
  10. Save as a new Gaussian input file.

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