I’m wondering if running MD simulations locally would be viable.
I’m using GROMACS to simulate a protein-ligand complex, where the protein is between 400 to 900 amino acids in size.
I’d like to run a 100 ns production MD o a MacBook.
Is it feasible to run this locally (realistically)? If not, would it be better to use the Mac just for testing, preparation, and minimization?
Any advice on performance, limitations of macOS for GROMACS, or optimization tips would be much appreciated!
Thanks in advance!
There’s nothing technical stopping you from doing so (aside from how much time you’re willing to spend, how much storage space you have on the macbook), and you can try out a shorter simulation of the system to get a sense of how long it will take and how much memory it takes up. A 100 ns of a 400-900 atom protein on a macbook I’m guessing will take a week or two to complete. If it’s a one-off simulation, you don’t have access to additional computing resources and your macbook has sufficient storage space, there’s nothing stopping you from trying it out.
It’s likely not realistic to be running regular simulations on a macbook due to limited storage capacity and the amount of time you’ll need to wait for the simulations to run, not to mention how quickly such an approach would burn through the macbook’s lifespan. If you do have access to additional computing resources, use them, even for the minimization and equilibration steps. I personally don’t think it’s realistic to expect any significant or useful results from such simulations when you’re constrained to running them on a macbook.
Just to clarify —if I will run the simulation on a Mac Studio, not a MacBook. I understand from your message that while it’s technically possible to run a 100 ns simulation of a 400–900 residue protein-ligand complex on a personal machine, it’s not ideal on a MacBook due to storage, speed, and wear concerns.
Given that the Mac Studio has significantly more power and storage than a laptop, do you think it would be a more realistic option for occasional or one-off simulations — especially when access to external computing resources is limited or delayed?
I really appreciate your insight and just want to make sure I fully understand the trade-offs
I’m not familiar with the differences between mac studio vs macbook, and I can’t really judge for you what the best way to use your resources are, I’d say try out a 1 ns simulation and check the amount of storage space it ends up using and the rate at which the simulations have run in the log file, that should give you a better idea of what you’re working with