Closed nitroamos closed 6 years ago
This might be related to https://github.com/pandegroup/openmm/issues/2025. I was never able to reproduce it in that case, but maybe I'll be able to with your files.
it's not consistent, you may have to try a couple times...
also, since there's a random number generator involved, you might consider (if practical) exposing the seed as a parameter. not sure how portable that would be, but it might help with debugging.
I tried four times, but wasn't able to reproduce the problem. It sounds like something is going wrong in the energy minimization step.
You said yesterday in #163 you had installed the latest dev build. By any chance did that fix this problem? I recently made some changes to make energy minimization a bit more robust, so it's possible that's why I'm not seeing it.
Yes, I wrote up this issue before switching to the dev branch. I've run the test many times now and haven't seen a problem (and even did a switch back to prod for positive control) so I think you fixed it. Thanks!
Great! For future reference, this is the change that I think probably fixed it: https://github.com/pandegroup/openmm/pull/1984
Hi, I'm trying to run PDBFixer on 2x2v. I think I'm using the latest of OpenMM and PDBFixer. I downloaded a fresh pdb from rcsb and then ran this script (as recommended by your manual):
sometimes hydrogen placement appears ok, other times it's wild, e.g. (full pdb below):
If it matters, I think the machine I'm running on has a GPU (based on a stack trace I saw from PDBFixer on this system when adding a membrane).
Any ideas on what I might try?
output.pdb.tar.gz