quickmin-step 2024.5.7

Description:

quickminstep 2024.5.7

SEAMM QuickMin Plug-in






A SEAMM plug-in for simple, quick minimization

Free software: BSD-3-Clause
Documentation: https://molssi-seamm.github.io/quickmin_step/index.html
Code: https://github.com/molssi-seamm/quickmin_step


Features
QuickMin provides quick, simple optimization of molecular structures using one of a
number of forcefields. It is intended for small systems, with no more than about 300
atoms. Beyond that size it will be rather slow, but more importantly larger systems
typically have many local minima, often close to each other energetically, so the
concept of the minimum structure is not very useful.
QuickMin uses OpenBabel for the minimization. There are currently five forcefields
available:


GAFF – the general AMBER force field
MMFF94 – the Merck molecular force field
MMFF94s – the Merck molecular force field for energy minimization
Ghemical
UFF – Universal force field


The first four have parameters for organic and biomolecular systems, while UFF attempts
to cover the entire periodic table with reasonable accuracy. The more specialized
forcefields tend to be more accurate, roughly in the order listed (though the two MMFF94
are essentially similar). By default QuickMin will try each of the forcefields in the
order given until it finds one that can handle the given molecule. You can specify the
forcefield to use; however, if it does not have parameters for your molecule, QuickMin
will throw an error.


Acknowledgements
This package was created with the molssi-seamm/cookiecutter-seamm-plugin tool, which
is based on the excellent Cookiecutter.
Developed by the Molecular Sciences Software Institute (MolSSI), which receives funding
from the National Science Foundation under award CHE-2136142.



History

2024.5.7 – Bugfix: Corrected sign on gradients.

OpenBabel calls “forces” “gradients”, so needed to take the negative to get the
actual gradients.


2024.5.3 – Added single point energy and Results.json

Added control to allow a single point energy as well as optimization. This
supports using QuickMin with e.g energy scans.
Standardized the name of the energy to simply “energy” to better support other
plug-ins and codes understanding the results.


2023.11.15 – Bugfix: structure handling
Error putting the coordinates into a newly created configuration.

2023.10.30 – Enhanced structure handling.
Switched to standard handling of structures, which adds ability to name with the
IUPAC name, InCHI, and InChIKey in addition to previous methods.

2023.1.14 – Changed documentation to new style and theme.
Switched the documentation to the MolSSI theme and diátaxis layout, though more work
is needed.

2022.11.7 – Internal Release
Switching from LGTM code analysis to GitHub Actions using CodeQL, since LGTM is
shutting down!

2022.10.23 – Properties added
Added a single property, ‘total energy#QuickMin#<forcefield>’, to store the final
energy in the database. Also added ‘total energy’ as a result for tables or
variables.

2022.10.22 – Documentation!
Got the documentation into reasonable shape.

2022.10.20 – Initial Release!
Provides quick minimization for smaller molecules, using OpenBabel. Probably
reasonable for some few hundred atoms. Supports the following forcefields:


GAFF
MMFF94 & MMFF94s (which is optimized for minimization)
Ghemical
UFF


The default is the “best available” forcefield, which tries them in the order given
above until it finds one that can handle the molecule.