[gmx-users] Computational load of Constraints/COM pull force

[Kenny Goossens]

Dear all,


I am performing umbrella sampling simulations on gromacs 2018.3, and because I need to sample every frame for a long time, I am trying to optimize the settings I'm using to get the maximum performance from my cluster. However, whenever I try running benchmarks, I notice that the relative amount of computing time that it takes to calculate constraints and COM pull force vary wildly (within a range of 2-30%). As you can imagine, this has a dramatic impact on the performance, as my performance for identical runs can fluctuate between 20-90 ns per day. I'm not sure if this is a general problem, or if this is caused by something I'm doing wrong. Is anyone able to help me out with this? Thank you!


Kind regards,


Kenneth