I've been using "mixed" precision and have been assuming it's best since it was introduced. Now I'm testing it, and I'm finding that single precision is visibly faster (260 steps per second compared to 200 with mixed!) Still non-100% utilization is present though. However, on 1080 Ti, switching from...

hi Peter! Thanks for your advice. Before I dive deeply into this, I wanted to share some general stats with you. Running a simulation with 500k at volume density of 50% I'm getting 200 timesteps per second on 3080, and 140 timesteps per second on 1080 Ti. Interestingly, 1080 Ti has 100% GPU utilizat...

Hi Peter, We have been doing polymer simulations using OpenMM for many years now. We typically have fairly simple systems: 50k to 400k particles connected by harmonic bonds, simple repulsive potential between them, variable langevin integrator, and PBC or external confinement. Our polymers are typic...

Hi Peter,

Good to hear that the new version of OpenMM is coming out!

Will there be a variable version of a new Langevin Integrator? We got addicted to variable integrators for now!

Also, will you have support for cuda 11 and for Python 3.8?

Thanks,
Max

Thanks, Peter! That makes sense. Speaking of repeated bonds... in the past we've actually managed to add the same bond several times into the same force. We've also managed to create a bond of a particle with itself. Both were fine with OpenMM, but now we have some input checks on bonds and angles i...

In our polymer simulation library, we may end up in a situation where we have two copies of the same bondforce (e.g. Harmonic Bond Force), with some of the bonds defined in one copy and other bonds in another copy. Could this lead to any collisions inside OpenMM, or to a noticeable slowdown?

Thanks for a quick fix!

Thank you!

I thought of another workaround: randomize particle positions by a small value after minimization and before starting a simulation. It should be sufficient for now.

That makes sense! And that does affect the start of nearly every simulation we've done in the past, but for most of them it won't be a problem. I will work around this by running a fixed timestep integrator for this project, where precise alignment at the starting conformation is very relevant. It w...

I was troubleshooting the fact that our system ends up with a very large Ep and Ek after running local energy minimization, and I came across a very strange observation. I tried advancing the integrator step-by-step after running local energy minimization. I'm using Variable Langevin Integrator. Wit...