Emilio Gallicchio
Emilio Gallicchio
A personal note about HIP if you are still considering it. We have been playing around with the StreamHPC implementation https://github.com/StreamHPC/openmm and https://github.com/StreamHPC/openmm-hip. We were able to build and test...
I think in general the factor of N comes from the Jacobian of the coordinate transformation from Cartesian lab coordinates to dimensionless unit cell coordinates. If the centers of mass...
> How about the CUDA support questions? [...>] especially ones that provide new plugins. (@egallicc I'd value your perspective on that last part.) Sorry, I missed this. I think it...
We found a [workaround](https://github.com/Gallicchio-Lab/AToM-OpenMM/commit/be867de26bbf638576dc8c7db07167abf0f7e64a) for AToM-OpenMM that disables the NonbondedForce using force groups rather than removing it from the outer System. As a result, atom reordering appears to be triggered...
I also have been doubtful about the current strategy. However, I tried the reordering strategy in CustomCVForce() and did not resolve the poor performance. After some testing, I almost convinced...
Right. Our [workaround](https://github.com/Gallicchio-Lab/AToM-OpenMM/commit/be867de26bbf638576dc8c7db07167abf0f7e64a) is to enable reordering in the main Context by retaining the NonbondedForce in the System, but skipping its evaluation by placing into a force group which is...
Agreed. Here are some potential issues to think about: - If the inner contexts have only a NonbondedForce, they might need the full set of ForceInfo's from the main Context...
> @egallicc would you mind comparing power consumption to ns/day on HIP like I did, but without erasing `downloadCountEvent`? Then we can investigate whether HIP reached a genuine 1000 ns/day...
Dear Tanmoy @tanmoy7989 did you end up submitting a PR to openmmforcefields to build non-canonical protein residue templates? We are modeling a receptor with a covalent inhibitor, and we can't...
I am testing a likely useful prototype. I will share the script with anyone who commits to help add the feature to openmmforcefields. ;-)