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Another possibility is to invoke the QC experiment from another InSilicoLab experiment (e.g. Trajectory Sculptor). In such case geometries of the system may be passed between experiments and they are immediately available as input data in the QC experiment interface.
Setting-up the QC experiment
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The geometry of the system may be entered from a file loaded in the Molecule Specification section. The type of the file may be specified in the opening window.
The system and the requested calculations are specified in the Input Data Specification section.
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Structure of the system selected from the list may be visualized as an Jmol applet (Show in Jmol):
The software used in calculations can be selected from the list. Currently, three QC programs are supported:
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For example, the input for Gaussian ZINDO calculations of 30 lowest electronic excitations for a phenylalanine molecule in a solution using structures prepared in Trajectory Sculptor and requesting 512MB RAM for each job may read:
Job execution
Clicking the Run button creates the input files based on the supplied geometries and parameters entered in the Input Data Specification. The jobs are then submitted for execution to the PLGrid.
In the Job Execution Status section one may trace the progress of calculations. The job status changes from EXTERNAL through SUBMITTED and RUNNING to FINISHED.
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Results of finished jobs are used to update the table and the plot of SCF energy values:
For each job the Download job files list may be used to select and download the files associated with the job: input, checkpoint and output files as a single .tar.gz file or the XML file containing the results extracted from the output.
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To use the program its name needs to be selected from the list of programs in the Input Data Specification section:
Coordinates of the system can be entered in the Geometry Specification section. Uploaded geometry can be viewed as Jmol applet on clicking the molecule icon next to the file name. Butadiene molecule is used in the example.
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