General usage

How can I get started using AutoDock-GPU?

Best way to start running dockings using AutoDock-GPU in no-time is by following the guideline for users.

What was the main motivation for developing AutoDock-GPU?

Speeding up -- the typically-long -- AutoDock executions by leveraging the embarrassingly parallelism in its LGA implementation.

Preliminary development was part of the OCLADock project.

What is the difference between AutoDock-GPU and AutoDock4.2.6?

The AutoDock-GPU implementation involves modifications to the original AutoDock4.2.6 functionality in order to better exploit parallel processing, and the execution performance, without negatively affecting the docking quality. These modifications include the following:

• Arithmetic precision
• Arrangement of data structures
• Genetic selection scheme
• Specification of program arguments

For details, read the article describing the implementation details of AutoDock-GPU.

Can I run AutoDock-GPU on a multi-core CPU machine?

Definitely! One of the main program's feature is the functionality portability thanks to its OpenCL-based implementation.

Can I target other accelerator devices besides GPUs & CPUs?

While this should be possible, one should also bear in mind that performance portability with OpenCL is not a guarantee!

Devices with a significantly different underlying architecture might not benefit from a typical data-parallelization approach.

An example is OCLADock-FPGA that uses task parallelization for Intel FPGAs. The corresponding publication is available here.

Can I run AutoDock-GPU on Windows machine?

This shoud be possible right away, although this wasn't tested yet.

Enhancements

Does AutoDock-GPU support flexible rings?

Yes, similarly as in the original AutoDock4.2.6.

Corresponding development will be integrated into the mainline code soon.

Collaboration and support

I have ideas for further performance improvements, new features, and other suggestions

Ideas are always welcome!

If you have ideas or feature request, please add an entry under issues.

If you want to contribute, please read the contributor's guidelines and then create a pull request.

I need help for using AutoDock-GPU

Proceed as indicated here.

Further reading

Go to Wiki home.