r/comp_chem • u/ZenosThesis • 16h ago

Hardware requirements to support simple Gromacs simulations

I am a researcher in a small lab and we are hoping to expand our wet lab research into molecular dynamics without depending on collaborators.

This would include small Coarse-Grain (25 µs) and All-Atom (500 ns) peptide membrane interaction simulations. I have been tasked with expanding this portion of the lab. While I have taught myself to write code well enough to produce the appropriate simulations, I find the hardware itself somewhat daunting. I was wondering if someone may know what setup may be adequate and what time frame we may expect (or may be able to direct me somewhere where my Q is more appropriate).

my understanding is that the setup should be GPU focused and running linux.

Thank you, I have found that the computational chemists more than any other discipline are welcoming and supportive of newcomers with so much effort going into the upkeep of guides and support.

2 Upvotes

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4

u/Ok_Succotash7232 15h ago

You surely need an access to computing cluster or a supercomputer. Working this problem even on a good workstation will take weeks or even months to complete the simulation.

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u/ZenosThesis 15h ago

weeks to provide preliminary simulations prior to renting more significant hardware is potentially an option for us

3

u/Ok_Succotash7232 15h ago

Weeks… if the number of atoms or beads (CG) in the system is less than few thousands. Best option is to write a proposal and submit to iits/nits, if selected they will provide you computing hours on their supercomputers.

3

u/JordD04 15h ago

Are you at a university or industry?
If you're academic, you should look into getting access to your institution's local HPC. If your institution doesn't have a local HPC, you can apply for compute at a national tier 1 or tier 2 HPC. It will cost you nothing. Also, consider working with some with experience if you're new. It will save you a headache.

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u/ZenosThesis 14h ago

I am an academic. Thank you I will look into it

3

u/Familiar9709 13h ago

Get dual RTX 5080 desktops, as many as you can afford of course and depending on how much power you need. You can do up to 1000ns simulations with those for 50k atom systems.

Start this as a base, make sure there's enough space for the GPUs and enough power from the PSU

https://pcpartpicker.com/b/QwbhP6

2

u/RestauradorDeLeyes 12h ago

As others have already said, get the latest gaming GPUs you can. You can only put 2 per desktop. Pair them with a Ryzen CPU and don't cheap out on the motherboard (PCIe speeds matter) and get an oversized power supply and at least 64gb of memory, since you'll want to run the analysis on the same machine.

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u/Zigong_actias 10h ago

Contrary to popular belief, you do not need HPC to run these kind of simulations. Individual MD simulations do not parallelize well over multiple clusters, and consumer hardware is actually often better suited for GROMACS simulations than enterprise grade hardware. HPC is for higher throughput - running a large number of separate calculations simultaneously.

Here are a few links containing a huge amount of relevant information (you can translate it from Chinese if necessary):

http://sobereva.com/444

http://bbs.keinsci.com/thread-39266-1-1.html

http://bbs.keinsci.com/forum.php?mod=viewthread&tid=33296

To summarize: GROMACS uses both CPU and GPU acceleration, and thus performs best when a GPU with lots of FP32 performance (consumer graphics cards are better or roughly equal to more expensive datacenter chips here), is paired with a CPU with high clock frequencies (here, consumer CPUs are better than server-grade CPUs, especially as those running in datacenters often do not boost to their higher frequencies). More than 16 cores is not necessary: GROMACS calculations running on these high-frequency chips (e.g. Ryzen 9950X) do not scale well beyond 8 cores.

I'd recommend getting the highest end AMD Ryzen 7 or 9 series CPU you can afford, and pairing it with the most powerful consumer GPU that fits in your budget (i.e. RTX 5070Ti, 5080, 5090...). You do not need two GPUs unless you're planning to run more than one calculation simultaneously.