Release Notes¶

v 2.1.1 September 2023¶

A new cube type, Parallel Iteration Checker Cube, has been added to enable scalability of the (serial) Iteration Checker Cube.

In the Solvation Cube, the “geometry” parameter name has been changed to “Periodic Box shape.” The parameter offers two options: a “cubic” or “rectangular” periodic box.
The Iterative NPT Cube has a better way of setting trajectory intervals for long simulations (>= 10 ns).
The Ligand Charge Cube now supports ELF10 charge assignment of macrocycles.

Since the first MD pkg release, we have been using Pickle to serialize and deserialize MD custom objects passed along the OpenEye data records. A main side effect of pickling them is that the class objects API is embedded inside the produced dataset. Therefore, updating the object APIs could generate issues. To overcome the problem, all the MD custom objects are now using JSON serialization and deserialization, which does not have this side effect. To avoid compatibility problems, in this release both serializers (pickle and JSON) are supported. However, the support for pickle will be dropped in future releases, and only the JSON serializer will be kept. The MDAPIDatasetConverterCube can be used to convert old datasets into new datasets where the JSON serializer/deserializer is used.

Iterative NPT Cube. This cube performs NPT MD simulations in the cyclic MD Floe (Plain MD Floe) on the provided system. If the MD cycle is complete, the cube emits the record to the “success” port and if not, it emits the record to the “cycle_out_port” port.
Iteration Checker Cube. This cube checks if the MD cycle is complete. If the MD cycle is complete, it emits the record to the “true” output port, and if not, it emits the record to the “false” output port.

The MDAPIDatasetConverterCube has been updated to support the conversion from old pickle datasets to the new JSON serializer/deserializer
The ComplexPrepCube has been updated to raise a fatal error if the protein cannot been found.

MDSpeedChecker Cube. This Cube estimates the wall clock time a production run will require and if the estimated time exceeds the 12 hour time limit, the Cube will fail the job.

New Cubes for Long Trajectory MD support; these are Cubes to enable iterative Floes.
Package dependencies update
Minor bug fixing

MDProxyCube. The MD Proxy Cube runs chunks of MD simulations in cycles till the desired total MD running time has been reached
MDRecoveryRestartProxyCube. This Cube is able to restart or recover a previously run long MD simulation. It is used in association with the MD proxy cube.

All the MD Cubes are by default pinning g3 spot instances to improve reliability.