Autodock is widely accepted program to perform small molecule docking. Unfortunately, this program uses a single core, while other core of the machine remains idle. This way, we are not able to completely utilize the machine (computer's) resource. If all the cores of the machine could be used by autodock module, it would be time saving method to utilise maximum of computational resource.
Please advise for any possible procedure/method/script to utilise maximum computer resource during AutoDock simulations.
Hi,
You can do multi jobs in your multi-core machines.
I recommend AutoDock Vina unless you intend to handle metalloproteins.
Hi Ishikawa,
Thank you for your response. I appreciate your suggestions to use Vina. My issue is still unresolved: AutoDock Vina utilizes more computational resources, hence perform computational task in less time? Is that what you want to say?
Dear Sabahuddin,
Yes, Vina can take advantage of multiple CPUs or CPU cores on your system to significantly shorten its running time.
But, Autodock4 is better for metalloproteins, because Vina is not good at handling them.
The GPU version of Autodock can be available, I haven't tried it yet, though:
http://sourceforge.net/projects/gpuautodock/
http://autodock-software-in-parallel-with-gpus.soft112.com/
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