GROMACS version: 2023
GROMACS modification: No
In a previous post I said I had ran my first 20ns simulation in gromacs, and it took forever. I don’t remember exactly how long it took, but it was something along the lines 1.5-2 days for this simulation and I have a 12th Gen Intel(R) Core™ i7-12700H CPU with 14 cores, and a Nvidia GeForce RTX 3060 Laptop GPU. I had read on this and other forums that people be conducting 100-500ns simulation. And that’s not going above and beyond that like the standard for most researches. And I have to ask, do these people just have an unbelievable amount of patienece? Or is there a trick to running these simulations faster. Then I saw a forum asking in you need a super computer to run MD simulation and some guy was like, nah I can get 350ns/day in my setup, and another guy was like I get 1000ns/day with my setup. While on my computer I’d be lucky if I hit 15ns/day. I don’t know what’s the highest ns/day I’ve got but it definely not 350ns/day. So I was wondering If there is any configurations, techniques or something I could do to speed up or get better performing simulations like this guy?
It is possible that your settings are suboptimal (search “performance” on this forum for tips on bechmarking for the best settings).
However, a laptop CPU and GPU are likely power- and thermal-limited compared to a desktop or server computer, even if the chips look comparable on paper. (As you might know, the compute power is linked to the operating frequency the CPU/GPU, which is throttled down when the power delivery and temperature reach their maximum design limit. Because a laptop has physically less space for large heatsinks/fan and voltage conversion circuit, this necessarily lower than clusters/desktops)
Hi, it also depends a lot on how big is your system. How many atoms are you simulating? I guess 100-500ns/day would be achievable on a laptop only for relatively small systems (<10-20K atoms, maybe more if you don’t require PME?). In any case, I think this page is always very useful: https://manual.gromacs.org/documentation/current/user-guide/mdrun-performance.html