The beta of OpenMM 8.1 is now available. You can install it with conda using the command conda install -c conda-forge/label/openmm_rc -c conda-forge openmm This release contains many performance improvements, particularly to the CUDA and OpenCL platforms. The largest speedups are for very large syst...

If you want the particles to be completely immobile, you can just set their masses to zero. That will prevent them from moving at all.

I don't know of any specific numbers for it, but I'd expect the A10 to be significantly slower than the others.

The technical answer is that every Force class (or still more technically, the ForceImpl it creates) defines a getBondedParticles() method. It reports which particles are bonded to each other by that Force. In practice, the Forces that define bonds are HarmonicBondForce, CustomBondForce, CustomCentr...

I modified your script to loop over all platforms and time the force evaluation for each one. import numpy as np import openmm as mm from openmm import app from openmm.unit import angstrom import time positions = np.random.rand(110, 3) * 100*angstrom # define the box size box_size = 100*angstrom # d...

Another issue is your box size. 1000 nm is huge. The cost of PME scales with the size of the box. Do you really intend it to be that big?

What are you timing? The whole script, or just the call to getState()? All the setup is much more expensive than the force evaluation. Creating a Simulation involves a lot of work, but it only has to be done once. The very first call to getState() often also has to do additional initialization. That...

Modifying a System or the Forces it contains has no effect on any Simulations that already exist. You need to make the changes before you create the Simulation. Alternatively you can call simulation.context.reinitialize().

This error is unrelated to having multiple CustomNonbondedForces. It means a single CustomNonbondedForce has had multiple exclusions added to it for the same pair of particles.

You need to ask the Folding@home developers about this. I don't think they read this forum.