Failure to load charmm35_nowaters.xml in OpenMM 7.5 due to excessive memory use
Opened this issue · 4 comments
Originally identified in #164 but I didn't realize what the problem was at the time. This didn't occur in openmm7.4.2 but does in the current available version of openmm7.5. I haven't tested openmm7.6-beta yet.
In my experience this command:
forcefield = app.ForceField('charmm/charmm36_nowaters.xml')
never stops consuming more memory and never finishes loading, up to 32Gb of memory on a cluster.
@jchodera suggests it might be due to changes in ParmEd
and @peastman discovered that "it looks like something has gone wrong in the code to identify which patches to allow for which residues. https://github.com/openmm/openmmforcefields/blob/master/charmm/ffxml/charmm36_nowaters.xml includes over 100 <AllowPatch> tags for each standard residue. Compare to https://github.com/openmm/openmm/blob/master/wrappers/python/openmm/app/data/charmm36.xml which only has eight for most of them."
and @peastman discovered that "it looks like something has gone wrong in the code to identify which patches to allow for which residues. https://github.com/openmm/openmmforcefields/blob/master/charmm/ffxml/charmm36_nowaters.xml includes over 100 tags for each standard residue. Compare to https://github.com/openmm/openmm/blob/master/wrappers/python/openmm/app/data/charmm36.xml which only has eight for most of them."
The patch identification code uses this ParmEd code, so something must have broken in ParmEd.
@jchodera
Hi, sorry to bother, I am also having the same problem. In fact, I am getting the problem with all the chramm forcefields in openmmforcefields(I haven't tested any other). Is there any update to this problem? I also tried generating the xml files myself with the scripts found here. That just gave empty xml files. Could you give a detailed instruction on how to generate them using those scripts? That would be very helpful in the mean time. I am currently trying to circumvent this issue by resorting to generating psf files using charmm and them running them in openmm.
Was this addressed in 11.2 September 2022 release??
I am experiencing the same problem (with OpenMM 8.0.0). Is there a way to fix it at the moment?