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bbye98 / mdcraft

A Python assistant for performing and analyzing molecular dynamics simulations of soft matter systems
https://mdcraft.readthedocs.io/
GNU General Public License v3.0
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[Functionality/Example usage] Module OpenMM #7

Closed aazocar closed 3 months ago

aazocar commented 3 months ago

This is part of JOSS review over at https://github.com/openjournals/joss-reviews/issues/7013

Regarding this module, there is good API documentation but potential new users of the software would benefit from having more extensive examples for the openMM system extensions and tools https://mdcraft.readthedocs.io/en/latest/api/mdcraft.openmm.system.html#module-mdcraft.openmm.system

Specifically, those mentioned in the paper: add_image_charges and add_slab_correction

Another related aspect, is the Gaussian core model with smeared electrostatics (GCMe) mentioned on the paper, but it is not clear where this can be found on the API docs.

pw0908 commented 3 months ago

A few updates on this issue:

  1. @bbye98 Has added an extensive example going over the GCMe forcefield within the docs.
  2. As mentioned in an earlier comment in the paper issue, there is an extensive set of examples given in this repository using mdcraft. This is something the other reviewer has mentioned and, although we are discussion the option of simply referring to this repository within mdcraft, we can move some of these examples over if you believe it is necessary.
  3. Trying to match the naming scheme in LAMMPS and OpenMM, the GCMe forcefield can be found here in our API docs.
aazocar commented 3 months ago

I have now taken a deeper look into the new example and the other repository you mentioned with further examples. I was able to see the usage on the image charges and slab correction functions from openmm.system. With this I think all functionality is demonstrated and accessible with example usage.