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Right now planckton-flow does not allow custom forcefields to be made. It would be nice to change this for new molecules we create in mbuild.
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This is probably something to do with the prmtop files passed to MMPBSA.
There are som exciting challenges with alternative forcefields that still need to be considered in the parmconv tool but this…
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On line 2830 of the file src/forcefields/forcefieldmmff94.cpp, there is a typographical error. Instead of Cb=GetZParam(b), it should be Cb=GetCParam(b);
2829: Za = GetZParam(a);
2830: Cb = GetZ…
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This issue is a roadmap for Molly.jl development. Feel free to discuss things here or submit a PR. Bear in mind that significant refactoring will probably occur as the package develops.
### Low han…
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In setting up a variety of systems for simulation I came across one with a thioether bond (something I haven't encountered before in a protein I'm trying to simulate). The PDB structure is https://www…
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It would be really useful for a wide variety systems of it was possible on an input level to parse nucleotides, would that be possible at all ? It seems like a small modification (relatively speaking)…
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There are a handful of files in [`openff/toolkit/data/test_forcefields`](https://github.com/openforcefield/openff-toolkit/tree/master/openff/toolkit/data/test_forcefields) that have seem to have been …
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**Describe the bug**
Recently migrated to new computer, needed to recreate openff-related Git repos and conda environments to continue projects. Some packages (most notably openff.units and pint) hav…
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### Is your feature request related to a problem? Please describe.
At the moment, the particle system used in Resonite is a hybrid of Unity's system with some custom code for handling emissions and c…