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In the case where you have a default link which is made up of a sum of several potentials, i.e.:
```
[ link ]
resname $protein_resnames
[ dihedrals ]
-BB BB +BB ++BB 9 0 10 1
-BB BB +BB ++BB 9…
Lp0lp updated
3 months ago
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Is it possible to assign distance/angle/dihedral-Representation to non atom elements but to custom objects?
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Subclasses of `Connection` should have a function `measure()` that measures that bond/angle/dihedral. This will be good for sanity-checking your simulation.
Things to consider:
* How we want to im…
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See conversation in #67.
I see two possible implementations. One is to have `geometry.dihedral` be able to recognize the two cases, the other is to have a separate function.
The 2 independent pl…
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**Description**
Please describe the behavior you would like added to Interchange.
Various things we've discovered about lammps files that are requiring/using some post-generation modification we w…
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### Is your feature request related to a problem? Please describe.
I'm interested in integrating the xTB into a package for the automatic procedure and it would be good if one could do a geometry opt…
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With the merge of PR #2706 , the performance of the Ramachandran analysis tool improved markedly. It would be nice to see the improvements in the automatic [performance benchmarks](https://www.mdanaly…
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Hi, I generated a hybrid topology of two ligands, the [ dihedrals ] section of the hybrid topology looks like this:
[ dihedrals ]
; ai aj ak al funct c0 c1 …
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If a `parmed.Structure` has multiple dihedral potentials for a single set of atoms, then this information is lost in the conversion to the `gmso.Topology`.
I have put together a [gist](https://gis…