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GROMACS: gmx rms, version 2020.1-Ubuntu-2020.1-1
Hello,
I am currently running an MD simulation and am fairly new to all of this. Is there a way to run mulitple simulations from my ubuntu gromacs version? My simulation said it will not finish until next week and I have many to run, but I am afraid to press anything in fear it will stop my current run. And if there is a way to do this, can you direct me on how to? Thanks
Heather
Hi
Yes, it is possible to run multiple simulations at once but each simulation will take longer to complete since it will share resources with other runs. If your job is currently set to complete in a week, running four simulations at once may take each of them up to a month (although this depends on a lot of factors). You’ll have decide if you’re gaining anything from it.
If so, you can see this page in the manual for some information about how to control your simulations.
In particular, unless you’re using MPI, the mdrun options -nt sets how many threads to use so if you have a 8 CPU cores available and want to run 4 jobs you can set this to 2 for each job. But then you should also use the -pin and -pinoffset to maximize your performance. That page has a lot of information and examples for that, depending on your setup.
If you want a more specific answer it’d help to know more about your computer. How many CPU cores does it have? Are you using a GPU for acceleration? How many jobs would you like to run at once?
On another note, there’s no risk in stopping your current simulation. You can resume it from its last saved checkpoint using the -cpi option for mdrun, and Gromacs saves this every 15 minutes and when stopping the simulation.
Petter