Hi Lee-Ping, I am working with an SGE submit system, and my experience has been exactly as you describe. I can submit a job and assign one core to it. SGE then counts that job as using one core in its accounting, and assumes that all the other cores are free. However, SGE does not actually restrict ...

Apologies for responding to you late. This has been a problem in simulations in computing clusters. If I set OPENMM_CPU_THREADS=1, then assign each simulation one cpu in my submit script, the OpenMM cpu overhead affects all the other jobs running in the same node, making some cpu threads entirely un...

When I run OpenMM on the CPU platform, I find that it routinely exceeds the CPU usage I set using the OPENMM_CPU_THREADS environment variable. For the included simulateAmber.py example, when I set OPENMM_CPU_THREADS=1, the cpu usage (from the top command) is usually between 130-150%. For 2 threads, ...

I will try that. Thanks!

I am trying to use the nonbonded forcefield in a vacuum simulation for large protein systems. In my simulations, I keep large domains of the protein system fixed in space, so there is not much point in calculating the nonbonded forces between atoms in the domains themselves. I am looking into creati...

That makes sense. Thanks!

I am looking at the various GBSA options available for use with OpenMM(6.2), with the Amber forcefield parameters, and I am left a little confused. I have been trying to use the python wrappers, and here is what I have discovered so far: 1. If I start with a pdb, then I can create a forcefield objec...