Merge pull request #1008 from openforcefield/doc-from-openmm

Improve documentation of `from_openmm` and related features

docs/index.md

@@ -29,6 +29,7 @@ using/collections.md
 using/migrating.md
 using/plugins.md
 using/status.md
+using/edges.md
 using/experimental.md
 
 ```

docs/using/edges.md

@@ -0,0 +1,33 @@
+# Sharp edges
+
+## Quirks of `from_openmm`
+
+### Modified masses are ignored
+
+The OpenFF Toolkit does not support isotopes or atomic masses other than the values defined in the periodic table. In the `Topology` and `Molecule` classes, particles masses are defined only by their atomic number. When topologies are read from OpenMM, the particle mass is ignored and the atomic number of the element is read and used to define the atomic properties.
+
+As a consequence, any hydrogen mass repartitioning (HMR) applied to a system is "un-done" upon import --- mass is shifted back from hydrogens to their heavy atoms. To re-apply HMR (shift masses back to hydrogens), use the appropriate API at export time, typically with an export method's `hydrogen_mass` argument.
+
+For updates, [search "HMR" in the issue tracker](https://github.com/search?q=repo%3Aopenforcefield%2Fopenff-interchange+hmr&type=issues&s=updated&o=desc) or raise a [new issue](https://github.com/openforcefield/openff-interchange/issues/new/choose).
+
+Keywords: OpenMM, HMR, hydrogen mass repartioning
+
+### Force constants of constrained bonds may be lost in conversions
+
+Commonly, OpenMM systems prepared by other tools constrain bonds (i.e. bonds between hydrogen and heavy atoms) and/or use rigid water models. These topological bonds lack force constants, which are required by some other engines even though they do not affect the behavior of the simulation.
+
+For example, consider an OpenMM system prepared, from the OpenMM API, with `ForceField.createSystem(..., constraints=HBonds, rigidWaters=True)` and then imported with `Interchange.from_openmm`. The constrained bonds, including all bonds in waters, don't contain physics parameters (particularly the force constant `k`). These parameters are typically dropped from the corresponding `HarmonicBondForce` when running OpenMM simulations with these sorts of constraints. When exporting this system to GROMACS or another engine that needs these parameters, the export will either crash due to missing parameters or silently write a file with some missing or blank parameters.
+
+For more, see [issue #1005](https://github.com/openforcefield/openff-interchange/issues/1005#issue-2405679510).
+
+Keywords: OpenMM, GROMACS, constraints, bond constraints, rigid water
+
+## Quirks with GROMACS
+
+### Residue indices must begin at 1
+
+Whether by informal convention or official standard, residue numbers in GROMACS files begin at 1. Other tools may start the residue numbers at 0. If a topology contains residue numbers below 1, exporting to GROMACS will trigger an error (though not necessarily while exporting to other formats). A workaround for 0-indexed residue numbers is to simply increment all residue numbers by 1.
+
+For more, see [issue #1007](https://github.com/openforcefield/openff-interchange/issues/1007)
+
+Keywords: GROMACS, residue number, resnum, residue index

openff/interchange/components/interchange.py

@@ -429,6 +429,12 @@ def to_openmm_system(
         system : openmm.System
             The OpenMM System object.
 
+        Notes
+        -----
+        There are some sharp edges and quirks when using this method. Be aware of some documented
+        issues in the :doc:`/using/edges` section of the user guide. If you encounter surprising
+        behavior that is not documented, please raise an issue.
+
         """
         from openff.interchange.interop.openmm import (
             to_openmm_system as _to_openmm_system,