Gaussian QM Run Input Files Successful Calculation

Running this Floe with the provided input file will cost around $0.40.

The input file for this Floe (enantiomers.tar) can be found in the “Gaussian QM Run Input Files” folder in the Tutorial Data on Orion. This tar file has two Gaussian input files for 2-Chloro-1,2-difluoroethanol: rr_input.com and ss_input.com corresponding to the R,R and S,S enantiomers respectively. The output from this Floe will let you compare the electronic Circular Dichroism spectra (ECD) of the two enantiomers.

Locate and Run the Floe

Navigate through the categories Product-based / Quantum Mechanics / Gaussian to find this Floe. Then, locate or search for “Gaussian QM Run Input Files.”

This Floe takes any Gaussian files (extension .com or .gjf) or an archive with multiple Gaussian files as input (help organizing tar files). In this tutorial, the enantiomers.tar file from the Tutorial Data on Orion is used for the “Gaussian Input Files” parameter.

By default the hardware requirements for Gaussian calculations are set to 8 CPUs, 14.4GB memory, and 25.6GB disk space. These parameters are meant to be more than sufficient for most drug like molecules with most basis sets. However, for large calculations you may need to increase these requests. Press the “start job” button to begin the calculation:

Input Form

By navigating to the jobs tab and selecting the running job, you can see the job details including current cost and any written outputs. By selecting job parameters at the top, you can see changes to parameters in this job compared to floe default setting. The floe diagram on the right shows progress in the Floe: gray, orange, and blue colors represent the completed, in progress, and the pending tasks, respectively.

Running Gaussian QM Run Input File Floe

Download and Analyze Results

Once the job is finished, the job details will show final cost and wall clock time. The generated outputs are shown in the “Results” section at the top left. This Floe only generates files, so you must select the “show non-dataset files” box to see the completed files. The results can be downloaded directly from here by clicking on the down arrow next to each file.

Note

Files can also be downloaded from the data tab by clicking on the ellipses to the left of the file and choosing “Download.”

For this tutorial there should only be one output file, we did not change the name when submitting the job so it is called Gaussian_output.tar. If some or all of the calculations failed there would be a Gaussian_failures.tar file. For an example with failure output, see the Gaussian QM Run Input Files Failed Calculation tutorial.

Completed Gaussian QM Run Input File Floe

Download the Gaussian_output.tar file to your local machine. Unpack the tar file by double clicking on the file or from the command line withe the command tar -xvf [path to file] This will result in two directories, rr_input and ss_input. Both will contain a copy of the input file (.com) and the resulting output files (.log and .chk). The results from this Floe will always have the input file and a log file. Any other result files must be specified in the input file, such as the checkpoint files in this job.

unpacked output tar file

Note

Currently, Gaussian_output.tar must be downloaded for analysis. In this tutorial, GaussView is used on a local machine to view the results. In the future, more integration with the Orion UI will be available.

Open the rr_opt.chk file with GaussView. Select Results > UV-Vis to show the UV-Vis and ECD spectra for this enantiomer.

Calculation ECD in GaussView

Repeat the process above with the ss_opt.chk file. When we compare the ECD spectra, the two enantiomers have opposite changes in absorption. These can be compared to experimental results to understand the chiral purity of a sample.

Compare ECD Spectra for enantiomers