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CHARMM files seem to support `-` as an end-of-line continuation character.
Lines like [this](https://github.com/choderalab/openmm-forcefields/blob/master/charmm/toppar/stream/misc/toppar_ions_won.s…
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As per Alberto's request speed up
1. Solvation (divide and conquer approach to joining segments)
2. ~PDB writing (numba)~
So that it doesn't take 2 hours on 1million atoms systems (which appare…
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I want to use the Charmm36 force fields. I can add it, I'm just making sure that no one has done it yet.
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I think ionize() can be made to accept standard PDB names instead of ff-specific ones, so it's one less thing to worry about when switching ff. I think the builders already have all the aliases in pla…
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It appears we have another critical force field error: disulfide bonds don't work in CHARMM36 either. They're supposed to be handled by the DISU patch, but that patch somehow was omitted from the con…
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I made a test system with only 2 sodiums whose periodic distance should be shorter than the non-periodic. For some reason when I set up the system with periodic box, the electrostatic energy goes down…
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We may have wildcards
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This would be a nice feature. We should generate a bunch of large membranes and then trim and remove lipids within a certain distance to the protein. VMD can generate arbitrarily large membranes.
F…
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I was under the impression that dihedral types were sorted in parmed as per: https://github.com/swails/ParmEd/blob/a79adc8541d3156e099ba996febda1babddd3338/parmed/charmm/psf.py#L614 for PSFs
However …