Solubility Analysis Panel

Solubility Analysis Panel Features

• Summary tab
  • System details section
  • Molecule information section
  • Results section
  • 2D structure display
• Free Energy tab
• Exchange Density tab
• Molecular Environment tab
• Generate PDF Report button
• Save Image button

Summary tab

Display information on the simulation results for the chosen molecule.

System details section

This section supplies information on the job name, job type and molecule name.

Molecule information section

This section supplies information on atom and bond counts, mass, charge, and formula.

Results section

This table lists the free energy values obtained in the hydration and sublimation simulations. The dissolution free energy calculated from these values is reported below the table.

2D structure display

The 2D structure of the molecule is displayed to the right of the Results section.

Free Energy tab

This tab displays information on the free energy convergence. Free energy differences given in kcal/mol in hydration and sublimation legs are plotted as a function of time. Three plots for each leg show the accumulated data during different time window schemes: forward; reverse; and sliding window.

Exchange Density tab

This tab displays charts showing the replicas and how they are exchanged between lambda windows. The charts for the hydration leg and the sublimation legs are shown on the left; selecting one of the charts displays it in the larger plot on the right, along with the color legend for the lambda windows.

Each replica is color coded and the plot shows how it occupies different lambda windows during the course of the simulation. The height of a color block for a given replica and lambda window represents the fraction of time the replica spent in the lambda window. Ideally each replica will sample all lambda windows uniformly; however non-uniform sampling is sufficient in most instances.

Molecular Environment tab

Display a bar chart of the average number of interactions of various types for the molecule that is being removed in each sublimation leg. The interactions that are monitored are: hydrogen bonds; intramolecular hydrogen (iH) bonds; halogen bonds; pi-pi; pi-cation, and hydrophobic interactions. To improve the clarity and the readability of the plot, the number of hydrophobic interactions is scaled down by a factor of 10.

Generate PDF Report button

Generate a PDF file that reports all of the information presented in the panel, with plots, and includes explanatory text. Opens a file selector, so you can navigate to a location and name the file.

Save Image button

Save an image of the plot in the current tab, in PNG or JPEG format. Opens a file selector, so you can navigate to a location and name the file.