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SEAMM Packmol Plug-in

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PyPi VERSION

A SEAMM plug-in for building periodic boxes of fluid using Packmol

This plug-in takes the molecule in the current system and creates a periodic box containing many copies of the molecule in order to simulate a fluid.

Features

  • Multiple ways to specify final cell:
    • Size of the cubic cell and density or number of molecules or number of atoms.
    • Volume and density or number of molecules or number of atoms.
    • density and size of the cubic cell or volume or number of molecules or of atoms.

Acknowledgements

This package was created with Cookiecutter and the molssi-seamm/cookiecutter-seamm-plugin project template.

Developed by the Molecular Sciences Software Institute (MolSSI), which receives funding from the National Science Foundation under awards OAC-1547580 and CHE-2136142

packmol_step's People

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dependabot[bot] avatar doaa-altarawy avatar emarinri avatar paulsaxe avatar seamm avatar

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packmol_step's Issues

Initial Update

The bot created this issue to inform you that pyup.io has been set up on this repo.
Once you have closed it, the bot will open pull requests for updates as soon as they are available.

Issue with ions created using SMILES

  • packmol step version:
  • Python version:
  • Operating System:

Description

Trying to add Li+ as a structure

What I Did

defined the SMILES as [LiH0] or [Li+] In both cases added it added an H atom
Same for [PH0](F)(F)(F)(F)(F)F or anion analog.

Missing citations

  • packmol step version: 2020.9.29
  • Python version: any
  • Operating System: any

Description

There are no citations added to the citation database for either the plug-in or Packmol

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