Dear all,
I'm currently in conversation with my PI to get a PC mainly for protein modeling and MD simulations.
One of the software for protein modeling I want to use is rosetta, but unfortunately, I don't know what component I should focus on. RAM/CPU/GPU? all three of them?
I hope someone can help me.
Thanks in advance.
Best regards,
Carlos
ps- I don't have a specific budget yet, so feel free to suggest to me the best configuration you can think of.
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Hi!
I'm commenting mostly because I need to do the same and PC parts are also not my forte. I can give general guidelines that I'll be considering in an upcoming build...
Hope this helps. Please share what you end up buying!
Rosetta minimums out at about 2GB per process when using it in MPI mode (and caps far higher depending on protein size) - RAM needs scale very strongly with protein size. You can go a lot lower with multithreading but only a few applications use multithreading. Almost nothing in base Rosetta uses the GPU, but the RosettaDL stuff mostly does use GPU.
Unfortunately "Rosetta" is not a sufficient specification to know what compute resources you should use. I've run jobs that used 1 processor and 200 GB of RAM; I've run jobs that used 10000 processors at once. Some jobs can run on your laptop or even your phone, some should be run on dedicated supercomputers. I'd recommend getting something big enough to run "test scale" jobs to make sure you are doing the experiment you mean to, and then farming out the real work to academic super compute time acquired via grants.