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mosdef-gomc

A hierarchical, component based molecule builder

https://github.com/umesh-timalsina/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
    3 of 6 committers (50.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (15.0%) to scientific vocabulary
Last synced: 6 months ago · JSON representation ·

Repository

A hierarchical, component based molecule builder

Basic Info
  • Host: GitHub
  • Owner: umesh-timalsina
  • License: other
  • Language: Python
  • Default Branch: master
  • Homepage: https://mbuild.mosdef.org
  • Size: 73.8 MB
Statistics
  • Stars: 0
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Created almost 4 years ago · Last pushed over 3 years 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.

Installation

The MoSDeF-GOMC package is available via conda:

conda create --name mosdef_gomc -c conda-forge mosdef_gomc

Owner

  • Name: Umesh Timalsina
  • Login: umesh-timalsina
  • Kind: user
  • Location: US
  • Company: Vanderbilt 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: "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

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Last synced: 9 months ago

All Time
  • Total Commits: 114
  • Total Committers: 6
  • Avg Commits per committer: 19.0
  • Development Distribution Score (DDS): 0.351
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Top Committers
Name Email Commits
bc118 c****8@g****m 74
Umesh Timalsina u****a@v****u 23
pre-commit-ci[bot] 6****] 14
Justin Gilmer j****r@v****u 1
Jenny 3****l 1
Tim Moore t****e@v****u 1
Committer Domains (Top 20 + Academic)
vanderbilt.edu: 3

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