pbuslaev

Rework are_isomorphic method of Molecule class for polymers

9

**Is your feature request related to a problem? Please describe.** `are_isomorphic` method of `Molecule` class is slow for large polymers. This can be a problem when importing `Topology` from `openmm`....

Interchange.to_gromacs() creates a topology with far too many atomtypes, which influences GROMACS performance

4

**Description** When dumping the interchange to GROMACS format, too many atom types are created. This is completely fine in terms of compatibility with GROMACS, but it is causing huge memory...

Predefined solvent component

4

I wonder if there is a way to generate a `SolventComponent` from a predefined structure? A use case might be a system with crystalographic waters, crystalographic ions, and cofactors, or...

This should solve #1937

[`Trajectory.atom_slice` method](https://github.com/mdtraj/mdtraj/blob/1748df86e8c56968ad129b151ff3ce0f5e67617e/mdtraj/core/trajectory.py#L2006) attempts to generate a subtrajectory for the atom slice. However, if the `atom_indices` parameters are not sorted, this can lead to an error. What the method does is...

Added simple rounding error solution

2

### Description This is a proposed solution for #1166 on the GROMACS writer side. If this approach is approved I can add tests/parameters ### Checklist - [ ] Add tests...

Adjust charges written to GROMACS topology

4

**Description** I am using interchange to write topologies for lipids generated with openmm [`Modeller.addMembrane`](http://docs.openmm.org/latest/api-python/generated/openmm.app.modeller.Modeller.html?highlight=modeller#openmm.app.modeller.Modeller.addMembrane) method. Overall, my code looks like that: ```python from openmm.app import Modeller, PME, HBonds, ForceField, PDBFile...

`Constraints` collection is not treated when writing GROMACS topology

5

**Description** The issue is in a way related to #1166. At first, I was creating `openmm` `System` object with constraints set to `HBonds`. In the resulting lipid topology, I got...

[QUESTION] Area per lipid in membrane-protein complexes

4

**What is the topic of your question**: Usage **Add your question below**: Is there a pipeline to compute Area per lipid for lipids in membrane-protein complexes?

Guessing the psf format type for VMD written psf files is wrong

1

## Expected behavior ## When loading the psf file, which was written by vmd 1.9.2 (`VMD for LINUXAMD64, version 1.9.2 (December 29, 2014)`), the format is not guessed correctly. The...