CODEWITHSUNDEEP
simulationbioinformatics
Abhinav Sharma
Abhinav Sharma

Reputation: 1

To do molecular dynamics simulations for my original protein (887 aa) and 2–3 of its variants with rtx 3050 laptop

I'm considering running molecular dynamics (MD) simulations for my original protein (887 amino acids) and 2–3 of its variants. However, I'm unsure if my laptop with an RTX 3050 GPU would be sufficient for these simulations. Could you provide some insights on whether this setup would be adequate, or if I might face significant limitations?

Many people gave vague replies but i want a valid source

Upvotes: 0

Views: 26

Answers (1)

dthorbur
dthorbur

Reputation: 1091

The reason people have been vague is likely because your question is incredibly vague.

Missing details:

  • You only say molecular dynamics, but now which type, or what tools you are thinking about using.
  • You only state the size of your protein, and now how many will be simulated at a time, or if there are other ligands/proteins/solution.
  • You only state the GPU, but CPU and RAM are often used for data loading and are also important in consideration.
  • You haven't said how much VRAM your RTX3050 has, it looks like it's 4GB though but there may be other versions I missed from a quick google.

Conclusion

With all of that said, yes, it's unlikely this setup would be sufficient to do almost any GPU-accelerated work.

4Gb of VRAM doesn't get you very far, especially with a protein as large as the one you want to use. The only silver lining I could see is the GPU is Ampere architecture, so it should be supported by most tools.

You can run some MD tools on a CPU provided enough RAM, but it would take days rather than hours. To save yourself time, my recommendation is try to get access to a GPU with at least 12-24Gb of VRAM for MD simulations for a protein of 900 peptides. GCP and AWS usually offer some free credits for new users.

Upvotes: -1

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