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.