GROMACS version:2024.5
GROMACS modification: No
I am asking for computer specifications for a Linux system to perform molecular dynamics (MD) simulations using GROMACS.
I will run membrane MD simulations of a docked complex. My ligand is a 60-nucleotide DNA, and my protein is a 676 aa ( homotrimer, each monomer with 676aa). The total number of atoms, including docked complex, lipid, ions and water, is about 500,000 atom. What is the best computer for this task, and how many GPUs should I use?
This is quite a large system for a single node/workstation. It might be better for you to rely on some HPC facility so that you can run multiple replicas at the same time.
That being said, I think you will need a good GPU (RTX 4090 possibly) and a good processor (like AMD Ryzen 9 9950X 16-Core Processor if you want to stick to “budget friendly” avoiding large server ones like the threadrippers). Hard to estimate in general the speed you are going to achieve, but with 500K atoms I would expect ~100ns/day with standard integrator and timestep.
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Thanks so much for your helpful comments!
I’ve decided to consider the following specifications:
[Processor & GPU]
- Intel Core i9-13900K (24 cores, 32 threads, 36MB Intel Smart Cache, base frequency: 2.2 GHz, max turbo: 5.8 GHz).
- NVIDIA GeForce RTX 4090 (24GB GDDR6X).
Do you think one GPU is sufficient?
Thanks again!
It depends on what you intend to run. On one GPU you usually run one simulation at a time. If you intend to go for long production runs of multiple replicas, then aim at getting access to an HPC facility, as (a single) workstation might be very limited for that, especially in the range of the medium-to-large systems size. Anyway, a RTX4090 is a very good GPU, you should be able to get good performance out of it.
Thank you very much for your advice. I truly appreciate your help.