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Hardware recommendations

PostPosted: Fri Feb 05, 2016 10:44 am
by aksharma
Hello,
I was wondering if there are any system recommendations for running virtual screening for a large library of ligands. I have experience with MD simulations, and my servers are dual processor machines with NVIDIA GPUs. I was wondering if it would be a good idea to invest in a quad-CPU system with higher thread count to run such a project. I am not sure if VINA uses GPU at all. Any recommendations/advice are highly appreciated.

Re: Hardware recommendations

PostPosted: Sat Feb 06, 2016 3:20 am
by sargis
aksharma wrote:Hello,
I was wondering if there are any system recommendations for running virtual screening for a large library of ligands. I have experience with MD simulations, and my servers are dual processor machines with NVIDIA GPUs. I was wondering if it would be a good idea to invest in a quad-CPU system with higher thread count to run such a project. I am not sure if VINA uses GPU at all. Any recommendations/advice are highly appreciated.

Hello and thank you for the message. For a large library of ligands, I recommend using Linux cluster. I had users who run virtual screening for a large library of ligands on a PC and it took them a couple of weeks to finish. It's a good idea to invest in a quad-CPU system with higher thread count. VINA can use all available CPUs 100%. Vina doesn't use GPU at all. I recommend starting with a smaller library of ligands to get an idea on how much time it would take to run larger library. It usually takes around 5min for one docking run to finish. If you have access to Linux cluster, it's better to run virtual screening there. The more nodes you have available in the cluster, the faster it will take to run virtual screening.