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mosdef-gomc

MoSDeF-GOMC: Python software for the creation of scientific workflows for the Monte Carlo simulation engine GOMC

https://github.com/gomc-wsu/mosdef-gomc

Science Score: 54.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    2 of 7 committers (28.6%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (15.6%) to scientific vocabulary
Last synced: 7 months ago · JSON representation ·

Repository

MoSDeF-GOMC: Python software for the creation of scientific workflows for the Monte Carlo simulation engine GOMC

Basic Info
  • Host: GitHub
  • Owner: GOMC-WSU
  • License: other
  • Language: Python
  • Default Branch: main
  • Homepage:
  • Size: 74.6 MB
Statistics
  • Stars: 16
  • Watchers: 4
  • Forks: 7
  • Open Issues: 5
  • Releases: 7
Created about 4 years ago · Last pushed 8 months ago
Metadata Files
Readme License Citation

README.md

pre-commit.ci status CI

MoSDeF-GOMC:

A User-Friendly Python Interface for Creating All of the files required to run a GPU Optimized Monte Carlo (GOMC) simulation engine via the Molecular Simulation Design Framework Molecular Simulation Design Framework (MoSDeF) (MoSDeF Github) software.

Overview

This Python code allows the auto-generation of the GPU Optimized Monte Carlo (GOMC) files for a simulation, which includes the coordinate (PDB), topology (PSF), force field (FF), and the GOMC control file. This software supports various systems, force field types, and can also create the PDB, PSF, and FF files for the NAMD simulation engine. Since MoSDeF-GOMC was built from the Molecular Simulation Design Framework (MoSDeF) (MoSDeF Github) platform, it provides complete integration with the MoSDeF software.

Warning

MoSDeF-GOMC is a new product continually adding functionality to provide an optimal user experience. Therefore, there could be some user-noticeable changes to this software when upgrading newer MoSDeF-GOMC versions.

The original version of MoSDeF-GOMC, which uses Parmed as the software backend, will be deprecated by December 2022. This Parmed version is already replaced with the new MoSDeF-GOMC version, which uses MoSDeF's GMSO software as the new backend. We recommend that the new GMSO version of MoSDeF-GOMC be used because it has many new features, and the Parmed is no longer supported.

Resources

Citation

Please cite MoSDeF-GOMC, GOMC, and MoSDeF tools, which are provided here.

Documentation

The MoSDeF-GOMC documentation is located here.

Installation

The recommended MoSDeF-GOMC package installation is with mamba:

conda create --name mosdef_gomc python=3.10

conda activate mosdef_gomc

conda install -c conda-forge mamba

mamba install -c conda-forge mosdef-gomc

The MoSDeF-GOMC package is also available via conda, but conda has had some issues pulling the most recent packages (user beware):

conda create --name mosdef_gomc -c conda-forge mosdef-gomc python=3.10

NOTE: conda has had some issues pulling the most recent packages, so a mamba installation is recommended.

Owner

  • Name: GOMC
  • Login: GOMC-WSU
  • Kind: user
  • Location: Detroit, MI, USA
  • Company: Wayne State University

Citation (CITATION.cff) 

# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!

cff-version: 1.0.0
title: >-
  MoSDeF-GOMC: Python software for the
creation of scientific workflows for the Monte
Carlo simulation engine GOMC."
message: "Please cite this software using these metadata and the preferred citation."
type: software
authors:
  - given-names: "Brad"
    family-names: Crawford
    affiliation: "Wayne State University"
    orcid: 'https://orcid.org/0000-0003-0638-7333'
  - given-names: Umesh
    family-names: Timalsina
    affiliation: "Vanderbilt University"
    orcid: 'https://orcid.org/0000-0002-5430-3993'
  - given-names: "Co D."
    family-names: Quach
    affiliation: "Vanderbilt University"
    orcid: 'https://orcid.org/0000-0002-1255-4161'
  - given-names: "Nicholas"
    family-names: Craven
    affiliation: "Vanderbilt University"
    orcid: 'https://orcid.org/0000-0002-4607-4377'
  - given-names: "Justin B."
    family-names: Gilmer
    affiliation: "Vanderbilt University"
    orcid: 'https://orcid.org/0000-0002-6915-5591'
  - given-names: "Clare"
    family-names: McCabe
    affiliation: "Vanderbilt University"
    orcid: 'https://orcid.org/0000-0002-8552-9135'
  - given-names: "Peter T."
    family-names: Cummings
    affiliation: "Vanderbilt University"
    orcid: 'https://orcid.org/0000-0002-9766-2216'
  - given-names: "Jeffrey"
    family-names: Potoff
    affiliation: "Wayne State University"
    orcid: 'https://orcid.org/0000-0002-4421-8787'

repository-code: 'https://github.com/GOMC-WSU'
url: 'https://github.com/GOMC-WSU'
repository: 'https://github.com/GOMC-WSU/MoSDeF-GOMC'
repository-artifact: 'https://github.com/GOMC-WSU/MoSDeF-GOMC/releases'
abstract: >-
MoSDeF-GOMC: Python software for the
creation of scientific workflows for the Monte
Carlo simulation engine GOMC

      MoSDeF-GOMC is designed to produce all the required files to run a Monte Carlo simulation, with only tens of lines of Python code.  Alternately, this software's output can also build the starting files for a single residue molecules via NAMD and and the py-MCMD codes.

keywords:
  - Python
  - Reproducibility
  - "Molecular Simulation"
  - "Monte Carlo"
  - GOMC
  - "computational chemistry"
  - chemistry
  - 'TRUE'
  - mosdef
license: "MIT"
preferred-citation:
  type: "article"
  authors:
  - given-names: "Brad"
    family-names: Crawford
    affiliation: "Wayne State University"
  - given-names: Umesh
    family-names: Timalsina
    affiliation: "Vanderbilt University"
    orcid: 'https://orcid.org/0000-0002-5430-3993'
  - given-names: "Co D."
    family-names: Quach
    affiliation: "Vanderbilt University"
    orcid: 'https://orcid.org/0000-0002-1255-4161'
  - given-names: "Nicholas"
    family-names: Craven
    affiliation: "Vanderbilt University"
    orcid: 'https://orcid.org/0000-0002-4607-4377'
  - given-names: "Justin B."
    family-names: Gilmer
    affiliation: "Vanderbilt University"
    orcid: 'https://orcid.org/0000-0002-6915-5591'
  - given-names: "Peter T."
    family-names: Cummings
    affiliation: "Vanderbilt University"
    orcid: 'https://orcid.org/0000-0002-9766-2216'
  - given-names: "Peter T."
    family-names: Cummings
    affiliation: "Vanderbilt University"
    orcid: 'https://orcid.org/0000-0002-9766-2216'
  - given-names: "Jeffrey"
    family-names: Potoff
    affiliation: "Wayne State University"
    orcid: 'https://orcid.org/0000-0002-4421-8787'
  title: "MoSDeF-GOMC: Python software for the creation of scientific workflows for the Monte Carlo simulation engine GOMC"
  year: "TBD"
  doi: "TBD"

GitHub Events

Total
  • Release event: 1
  • Issues event: 2
  • Watch event: 3
  • Delete event: 2
  • Issue comment event: 2
  • Push event: 4
  • Pull request review event: 1
  • Pull request event: 13
Last Year
  • Release event: 1
  • Issues event: 2
  • Watch event: 3
  • Delete event: 2
  • Issue comment event: 2
  • Push event: 4
  • Pull request review event: 1
  • Pull request event: 13

Committers

Last synced: almost 3 years ago

All Time
  • Total Commits: 165
  • Total Committers: 7
  • Avg Commits per committer: 23.571
  • Development Distribution Score (DDS): 0.406
Past Year
  • Commits: 138
  • Committers: 4
  • Avg Commits per committer: 34.5
  • Development Distribution Score (DDS): 0.319
Top Committers
Name Email Commits
bc118 c****8@g****m 98
pre-commit-ci[bot] 6****]@u****m 28
Umesh Timalsina u****a@v****u 24
Brad Crawford 6****8@u****m 9
Co Quach d****7@g****m 4
Jenny 3****l@u****m 1
Justin Gilmer j****r@v****u 1
Committer Domains (Top 20 + Academic)
vanderbilt.edu: 2

Issues and Pull Requests

Last synced: 7 months ago

All Time
  • Total issues: 13
  • Total pull requests: 58
  • Average time to close issues: 2 months
  • Average time to close pull requests: 9 days
  • Total issue authors: 5
  • Total pull request authors: 5
  • Average comments per issue: 0.62
  • Average comments per pull request: 0.62
  • Merged pull requests: 47
  • Bot issues: 0
  • Bot pull requests: 9
Past Year
  • Issues: 0
  • Pull requests: 6
  • Average time to close issues: N/A
  • Average time to close pull requests: 6 days
  • Issue authors: 0
  • Pull request authors: 3
  • Average comments per issue: 0
  • Average comments per pull request: 0.0
  • Merged pull requests: 3
  • Bot issues: 0
  • Bot pull requests: 2
View more stats
Top Authors
Issue Authors
  • bc118 (14)
  • umesh-timalsina (2)
  • daico007 (1)
  • justinGilmer (1)
  • GregorySchwing (1)
  • CalCraven (1)
Pull Request Authors
  • bc118 (44)
  • pre-commit-ci[bot] (14)
  • umesh-timalsina (7)
  • daico007 (3)
  • jpotoff (1)
Top Labels
Issue Labels
Pull Request Labels
enhancement (1)

Packages

  • Total packages: 1
  • Total downloads: unknown
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 2
conda-forge.org: mosdef-gomc

A User-Friendly Python Interface for Creating All of the files required to run a GPU Optimized Monte Carlo (GOMC) simulation engine via the Molecular Simulation Design Framework (MoSDeF) software.

  • Versions: 2
  • Dependent Packages: 0
  • Dependent Repositories: 1
Rankings
Dependent repos count: 24.1%
Average: 46.5%
Dependent packages count: 51.5%
Forks count: 54.0%
Stargazers count: 56.3%
Last synced: 7 months ago

Dependencies

.github/workflows/CI.yml actions
  • actions/checkout v2 composite
  • codecov/codecov-action v3 composite
  • conda-incubator/setup-miniconda v2 composite
  • docker/build-push-action v2 composite
  • docker/login-action v1 composite
  • docker/setup-buildx-action v1 composite
Dockerfile docker
  • continuumio/miniconda3 4.10.3-alpine build
docs/requirements.txt pypi
  • anaconda *
  • ele *
  • gsd *
  • ipykernel *
  • ipywidgets *
  • lark-parser *
  • mock *
  • nbsphinx *
  • numpydoc *
  • requests *
  • sphinx *
  • sphinx_rtd_theme *
  • sphinxcontrib *
  • sphinxcontrib-svg2pdfconverter *
  • sphinxcontrib-video *
  • unyt *
  • widgetsnbextension *
environment.yml pypi
  • bump2version *
  • sphinxcontrib-serializinghtml *
  • sphinxcontrib-svg2pdfconverter *
  • sphinxcontrib-video *