Like other programs Adun has specific data that it creates and works on – these data-types are analagous to Word .doc files or Keynote presentations. Adun’s four data-types are called Systems, Simulations, Templates and Data Sets.
When you work with Adun you constantly create new instances of these data-types, for example new simulations.Adun stores all the data it creates in databases which are browsable via the database browser as shown in the figure below. As you can see it stores the same types of data together in one ‘folder’.
Systems represent molecules. This can be a single water molecule or a protein-ligand complex. They contain both the configuration of the molecule along with the interactions present in it and the properties of its atoms. The interactions and properties are defined by the force-field used to build the system. Each of a the interactions in a system e.g. bond interactions, electrostatic interactions, is characterised by a set of parameters e.g. equilibrium bond length, which are also defined by the force-field. The atoms properties include partial charge and Van der Waals radius.
Use the SystemAnalysis plugin to get in-depth information on the contents of a System.
Templates describe how to perform a particular type of simulation e.g. gas phase or explicit solvent. They define the systems in the simulation, how they are related, and the algorithms to use to simulate them e.g. the thermostat.
Simulations objects are the output of Adun simulation processes. They usually contain the energies and configurations of a series of snapshots (frames) recorded during the simulation. Additionaly if there is a topology change during a simulation – for example a change in an atoms properties or the addition or deletion of atoms – this will also be recorded. The EnergyConverter and ConformationConverter plugins can be used (via the Analyser) to inspect the information in a Simulation.
Coming soon …
Each piece of data in Adun’s databases was created from something and was probably used to create something else. Instead of having to remember what data was used to create what Adun tracks this information, which we call the data-web, for you. Here’s how you can see all the data used to create, and that’s been created using, a particular data object.
To view the relationships of a particular Adun data object:
- Select the data in the database browser.
- In the main menu go to Object->Properties. This opens the property panel.
- Click on the ‘References’ tab.
Data used to create the object have ‘Input’ in the ‘Relationship’ column while data created from it have ‘Output’. The ‘Client’ column tells you where the data is located. You can select and manipulate data in the Relationship table just like data in the browser. Try highlighting an entry and choosing Object->Analyse in the main menu.