Grid-based Visualization of Changes in Molecular
Structure
We selected the first fragment of the 3FLY protein to perform
optimization calculations using the Gaussian 09 package (Figure 12a).
The panel for input-file creation was used to initialize the input
parameters and preview or modify the file. After providing the necessary
information, including job name, CPU cores, and wall time, the RESTful
APIs can be used to dispatched the job to the appropriate queue. During
runtime, it is possible to use the visualization panel (Figure 12b).
The visualization panel shows the structure and the optimization plot,
which can be checked at any time while the job is running. Animation and
multiple view (Figure 12b-3) options allow different visualizations of
the molecule structure. Optimization plots, including energy and
root-mean-square curves, are shown at the right panel, and in the lower
panels, the console records the processes associated with data
processing (Figure 12b-1), whereas the molecule panel shows the geometry
information of the structure, and the criterion panel displays the
minimum optimization convergence criteria of the Gaussian optimization
calculation (Figure 12b-2). Initial checking of the calculations
downloads a results file from the HPCs for parsing by GridMol. The
visualization panel displays the 3D structure and associated
optimization curves, along with data benchmarks for use during
subsequent rounds of optimization.