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mbuild.Compound.energy_minimize() function fails if a GMSO formatted XML is used #1052

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bc118 opened this issue Aug 29, 2022 · 1 comment

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@bc118
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bc118 commented Aug 29, 2022

Bug summary

mbuild.Compound.energy_minimize() function fails if a GMSO formatted XML is used.

Code to reproduce the behavior

Make the mbuild.Compound.energy_minimize() function work for the GMSO formatted XML is used, just like the Parmed XML files.

Notes:

For now, the GMSO versions should at least support the LJ (12-6) potentials.

In the future, we should support the range of GSMO-supported non-bonded and bonded potentials. @daico007 suggested we may be able do this via HOOMD.

@CalCraven
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So there's three ways we can address the issue:

  1. Quick and Dirty (ff-utils): Use the tools in the forcefield_utilities package to convert the GMSO XML to a Foyer XML and then do the typical OpenMM method.
  2. Quick and Dirty (parmed conversion): Parameterize a GMSO object using the GMSO XML, then convert to parmed and use the OpenMM method (might take some API tuning to let us pass the ParmED object instead of the forcefield
  3. Difficult, yet expansive (HOOMD minimization): Use some other pythonic facing methods to get the energy minimization, that can take a direct GMSO object. Will give much more flexibility for the diverse expressions GMSO can support.

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