A common, and time-consuming, task in molecular simulation is creating entries for new molecules for a given force-field. The antechamber program from the Amber suite of tools handles most of the details of this process for Amber related force-fields. However to use it with Adun its output still needs to be converted to the FFML [...]
The user manual has been extend with an entry describing linking – this is the ability to initialise the state (i.e. coordinates/velocities) of molecules in a simulation with their state from a checkpoint in another simulation. For example if you were a simulating a protein you could initialise it with a configuration generated from a [...]
The current CVS of Adun now automatically threads nonbonded and Generalized Born calculations to multiple cores if they are available. The attached graph shows the speed-up for Gas phase and GB simulations of a 6500 atom protein. Since the threading only applies to certain calculations you don’t get a linearly scaling speed-up. Instead the expected speed [...]
The current CVS of Adun contains a beta version of Adun’s data-sharing implementation. This allows users of Adun to easily access data in others users databases and also to share data with other users. Two forms of sharing are supported: P2P sharing – This is for sharing with particular people Publishing – This is for [...]
A new guide on how to extend Adun’s GUI with scripts has been added and we’ve rearranged the existing scripting documentation to make it more accessible. See the Scripting item under Documentation in the side-bar for more (or click here)
The possibility of sharing simulation templates and results has been a missing feature in standard molecular simulations packages for many years. The usefulness of such collaborative approach is clear when comparing algorithms, validating simulations or building datasets of precomputed simulations. Realizing this problem, the Adun team realized years ago that the power of our software [...]
