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Add LayeredDihedral and LayeredImproper support

5

Closes #561. ## Checklist - [X] Class Definitions - [x] Topology Changes (WIP) - [x] Tests - [ ] Other changes to formats/external modules (May be suited for a different...

umesh-timalsina

I bumped into an interesting case in using GMSO `gro` writer. The system of interest is a monolayer sandwiched between 2 box of water on top and bottom. This system...

daico007

HOOMD writer in GMSO is incompatible with forcefields that parameterize connections by a mix of types and classes. Bug Report: ------------ The majority of the forcefields we have in the...

CalCraven

Issue with writing virtual sites via a lone pair

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For forcefields such as tip4p, we can read the forcefield, and virtual sites are treated just the same as a site. The virtual site is then assigned an atomtype just...

CalCraven

Add support to write out rigid water for GROMACS

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This stem from a discussion with Dr. Potoff, we probably want to add the support to write out rigid water (only) to gromacs top file soon. Specifically, writing out the...

daico007

gmso FF periodic dihedrals and impropers yield a unyt_quantity or unyt_array. unyt_quantity : if only 1 periodic value is provided (1 n-value per dihedral/improper). See the gmso_benzene_GAFF_1_n_values.txt for an example....

bc118

Modified RB and Periodic torsions

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- The RB torsion should just use C0 and not C0 * cos(psi)**0. Note this is changing the phi to psi. - The periodic torsion should just be similar to...

bc118

Abstract_Site_Representations

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# The goal of of this PR is to allow support of different site classes beyond the currently implemented `Atom` Class. This PR is linked to Issue #495, and further...

CalCraven

Add virtual templates

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Really primitive `VirtualSite` class. My plan was originally to inherit from the `Connection` class. However virtual sites are not technically connected to the other members, so I decided to create...

rmatsum836

MDAnalysis Interoperability

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I would like to open some discussion about using `MDAnalysis` glue. This would require conversions from `gmso.core.Topology` to some `MDAnalysis` object - probably `Universe`? It is an appealing idea to...

mattwthompson