Science Score: 67.0%

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
    Found 10 DOI reference(s) in README
  • Academic publication links
    Links to: acs.org
  • Academic email domains
  • Institutional organization owner
  • JOSS paper metadata
  • Scientific vocabulary similarity
    Low similarity (18.4%) to scientific vocabulary
Last synced: 6 months ago · JSON representation ·

Repository

Basic Info
  • Host: GitHub
  • Owner: lu1and10
  • License: lgpl-2.1
  • Language: C++
  • Default Branch: esp_dev
  • Size: 156 MB
Statistics
  • Stars: 9
  • Watchers: 1
  • Forks: 1
  • Open Issues: 0
  • Releases: 0
Created 10 months ago · Last pushed 8 months ago
Metadata Files
Readme License Citation Authors

README

This is a fork of the [GROMACS](https://github.com/gromacs/gromacs)
molecular dynamics software.
This fork includes custom modifications for the ESP(Ewald summation with
prolate spheroidal wave functions) method.

The ESP method code modifications main contributors:
* Jiuyang Liang
* Libin Lu
* Alex Barnett
* Leslie Greengard
* Shidong Jiang

More data files and detailed descriptions will be available shortly.
If you have any questions, please do not hesitate to contact me via email
at llu@flatironinstitute.org.

**Note:** This codebase is not an official version of GROMACS.
It is independently maintained and modified.

               Welcome to the official version of GROMACS!

If you are familiar with Unix, it should be fairly trivial to compile and
install GROMACS. GROMACS uses only the CMake build system, and our
installation guide can be found at
http://manual.gromacs.org/documentation/current/install-guide/index.html

Visit http://forums.gromacs.org/ for discussions and advice.
Report bugs at https://gitlab.com/gromacs/gromacs/-/issues
Of course we will do our utmost to help you with any problems, but PLEASE 
READ THE INSTALLATION INSTRUCTIONS BEFORE CONTACTING US!

There are also several other online resources available from the homepage, 
and special information for developers.

If you use GROMACS for research (or other purposes) make sure to reference
the correct version of the code. The CITATION.cff file next to this README
contains all metadata useful for citation.

If you are a developer, or change the source for any other reason, check
out http://www.gromacs.org/development.

                               * * * * *

GROMACS is free software, distributed under the GNU Lesser General
Public License, version 2.1 However, scientific software is a little
special compared to most other programs. Both you, we, and all other
GROMACS users depend on the quality of the code, and when we find bugs
(every piece of software has them) it is crucial that we can correct
it and say that it was fixed in version X of the file or package
release. For the same reason, it is important that you can reproduce
other people's result from a certain GROMACS version.

The easiest way to avoid this kind of problems is to get your modifications
included in the main distribution. We'll be happy to consider any decent 
code. If it's a separate program it can probably be included in the contrib 
directory straight away (not supported by us), but for major changes in the 
main code we appreciate if you first test that it works with (and without) 
MPI, threads, double precision, etc.

If you still want to distribute a modified version or use part of GROMACS
in your own program, remember that the entire project must be licensed
according to the requirements of the LGPL v2.1 license under which you
received this copy of GROMACS. We request that it must clearly be labeled as
derived work. It should not use the name "official GROMACS", and make
sure support questions are directed to you instead of the GROMACS developers.
Sorry for the hard wording, but it is meant to protect YOUR research results!

                               * * * * *

The development of GROMACS is mainly funded by academic research grants. 
To help us fund development, we humbly ask that you cite the GROMACS papers:

* GROMACS: A message-passing parallel molecular dynamics implementation
  H.J.C. Berendsen, D. van der Spoel and R. van Drunen
  Comp. Phys. Comm. 91, 43-56 (1995)
  DOI: https://doi.org/10.1016/0010-4655(95)00042-E
 
* GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable
  molecular simulation
  B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl
  J. Chem. Theory Comput. 4 (2008) pp. 435-447
  DOI: https://doi.org/10.1021/ct700301q

* GROMACS 4.5: a high-throughput and highly parallel open source
  molecular simulation toolkit
  Sander Pronk, Szilárd Páll, Roland Schulz, Per Larsson, Pär Bjelkmar,
  Rossen Apostolov, Michael R. Shirts, Jeremy C. Smith, Peter M. Kasson,
  David van der Spoel, Berk Hess, Erik Lindahl.
  Bioinformatics 29 (2013) pp. 845-54
  DOI: https://doi.org/10.1093/bioinformatics/btt055

* Tackling Exascale Software Challenges in Molecular Dynamics Simulations
  with GROMACS
  Szilárd Páll, Mark J. Abraham, Carsten Kutzner, Berk Hess, Erik Lindahl
  In S. Markidis & E. Laure (Eds.), Solving Software Challenges for Exascale,
  Lecture Notes for Computer Science, 8759 (2015) pp. 3–27
  DOI: https://doi.org/10.1007/978-3-319-15976-8_1

* GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers
  M. J. Abraham, T. Murtola, R. Schulz, S. Páll, J. C. Smith, B. Hess, E. Lindahl,
  SoftwareX, 1, (2015), 19-25
  DOI: https://doi.org/10.1016/j.softx.2015.06.001

There are a lot of cool features we'd like to include in future versions,
but our resources are limited. All kinds of donations are welcome, both in 
form of code, hardware and funding! Industrial users who choose to pay
for a license pro bono (it is still LGPL and can be redistributed freely) or
contribute in other ways are listed as GROMACS supporters on our webpages. 
Don't hesitate to contact us if you are interested.


                       Good luck with your simulations!

                              The GROMACS Crew

Citation (CITATION.cff)

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

cff-version: 1.2.0
title: GROMACS 2025.0 source code
message: >-
  If you use GROMACS, please cite it using the
  metadata from this file.
  To help us fund GROMACS development, we humbly ask
  that you also cite the research papers on the package,
  see https://www.gromacs.org/articles.html.
type: software
authors:
  - given-names: Mark
    family-names: Abraham
    orcid: "https://orcid.org/0000-0001-6363-2521"
  - given-names: Andrey
    family-names: Alekseenko
    orcid: "https://orcid.org/0000-0003-4906-7241"
  - given-names: Brian
    family-names: Andrews
    orcid: "https://orcid.org/0000-0003-4469-3147"
  - given-names: Vladimir
    family-names: Basov
    orcid: "https://orcid.org/0009-0008-3889-3891"
  - given-names: Paul
    family-names: Bauer
    orcid: "https://orcid.org/0000-0002-2268-0065"
  - given-names: Hugh
    family-names: Bird
  - given-names: Eliane
    family-names: Briand
    orcid: "https://orcid.org/0000-0002-5875-6682"
  - given-names: Ania
    family-names: Brown
  - given-names: Mahesh
    family-names: Doijade
  - given-names: Giacomo
    family-names: Fiorin
    orcid: "https://orcid.org/0000-0002-8793-8645"
  - given-names: Stefan
    family-names: Fleischmann
    orcid: "https://orcid.org/0000-0002-2122-536X"
  - given-names: Sergey
    family-names: Gorelov
    orcid: "https://orcid.org/0009-0007-1431-0068"
  - given-names: Gilles
    family-names: Gouaillardet
  - given-names: Alan
    family-names: Gray
  - given-names: M. Eric
    family-names: Irrgang
  - given-names: Farzaneh
    family-names: Jalalypour
    orcid: "https://orcid.org/0000-0001-5092-1914"
  - given-names: Petter
    family-names: Johansson
    orcid: "https://orcid.org/0000-0001-9160-2549"
  - given-names: Carsten
    family-names: Kutzner
    orcid: "https://orcid.org/0000-0002-8719-0307"
  - given-names: Grzegorz
    family-names: Łazarski
    orcid: "https://orcid.org/0000-0002-5595-371X"
  - given-names: Justin A.
    family-names: Lemkul
    orcid: "https://orcid.org/0000-0001-6661-8653"
  - given-names: Magnus
    family-names: Lundborg
    orcid: "https://orcid.org/0000-0002-0873-7854"
  - given-names: Pascal
    family-names: Merz
    orcid: "https://orcid.org/0000-0002-7045-8725"
  - given-names: Vedran
    family-names: Miletić
    orcid: "https://orcid.org/0000-0003-3981-8806"
  - given-names: Dmitry
    family-names: Morozov
    orcid: "https://orcid.org/0000-0001-9524-948X"
  - given-names: Lukas
    family-names: Müllender
    orcid: "https://orcid.org/0009-0008-4978-624X"
  - given-names: Julien
    family-names: Nabet
  - given-names: Szilárd
    family-names: Páll
    orcid: "https://orcid.org/0000-0003-0603-5514"
  - given-names: Andrea
    family-names: Pasquadibisceglie
    orcid: "https://orcid.org/0000-0002-1630-6982"
  - given-names: Michele
    family-names: Pellegrino
    orcid: "https://orcid.org/0000-0002-2603-8440"
  - given-names: Nicola
    family-names: Piasentin
    orcid: "https://orcid.org/0000-0003-2760-4640"
  - given-names: Daniele
    family-names: Rapetti
    orcid: "https://orcid.org/0000-0002-7193-5220"
  - given-names: Muhammad Umair
    family-names: Sadiq
    orcid: "https://orcid.org/0000-0001-5713-1149"
  - given-names: Hubert
    family-names: Santuz
    orcid: "https://orcid.org/0000-0001-6149-9480"
  - given-names: Roland
    family-names: Schulz
    orcid: "https://orcid.org/0000-0003-1603-2413"
  - given-names: Michael
    family-names: Shirts
    orcid: "https://orcid.org/0000-0003-3249-1097"
  - given-names: Tatiana
    family-names: Shugaeva
    orcid: "https://orcid.org/0009-0001-8147-0762"
  - given-names: Alexey
    family-names: Shvetsov
    orcid: "https://orcid.org/0000-0003-1140-5751"
  - given-names: Philip
    family-names: Turner
    orcid: "https://orcid.org/0009-0004-7127-0777"
  - given-names: Alessandra
    family-names: Villa
    orcid: "https://orcid.org/0000-0002-9573-0326"
  - given-names: Sebastian
    family-names: Wingbermühle
    orcid: "https://orcid.org/0000-0001-5949-148X"
  - given-names: Berk
    family-names: Hess
    orcid: "https://orcid.org/0000-0002-7498-7763"
  - given-names: Erik
    family-names: Lindahl
    orcid: "https://orcid.org/0000-0002-2734-2794"
identifiers:
  - type: doi
    value: 10.5281/zenodo.14846130
  - type: url
    value: >-
      https://ftp.gromacs.org/gromacs/gromacs-2025.0.tar.gz
    description: Download URL
repository-code: 'https://gitlab.com/gromacs/gromacs'
url: 'https://www.gromacs.org/'
repository: 'https://manual.gromacs.org/2025.0/index.html'
abstract: "GROMACS\_is a free, open-source and high-performance software suite for molecular dynamics simulation and analysis."
keywords:
  - molecular dynamics
  - molecular simulation
  - biomolecular simulation
  - high performance computing
  - free software
license: LGPL-2.1-or-later
commit: v2025.0
version: '2025.0'
date-released: '2025-02-11'

GitHub Events

Total
  • Watch event: 7
  • Delete event: 1
  • Public event: 1
  • Push event: 13
  • Pull request event: 2
  • Fork event: 1
  • Create event: 2
Last Year
  • Watch event: 7
  • Delete event: 1
  • Public event: 1
  • Push event: 13
  • Pull request event: 2
  • Fork event: 1
  • Create event: 2

Issues and Pull Requests

Last synced: 9 months ago

All Time
  • Total issues: 0
  • Total pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Total issue authors: 0
  • Total pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Top Authors
Issue Authors
Pull Request Authors
  • lu1and10 (1)
Top Labels
Issue Labels
Pull Request Labels

Dependencies

.github/workflows/build_cmake.yml actions
  • actions/cache v4 composite
  • actions/checkout v4 composite
python_packaging/sample_restraint/Dockerfile docker
  • gmxapi/gmxapi 0.0.7 build
docs/requirements.txt pypi
  • Pygments >=2.2.0
  • Sphinx >=4.0
  • breathe *
  • furo *
  • sphinx-argparse *
  • sphinx-copybutton *
  • sphinx_inline_tabs *
  • sphinxcontrib-autoprogram *
  • sphinxcontrib-plantuml >=0.14
python_packaging/gmxapi/pyproject.toml pypi
  • mpi4py *
  • networkx >=2.0
  • numpy >1.7
  • packaging *
python_packaging/gmxapi/requirements.txt pypi
  • Pygments >=2.2.0
  • Sphinx >=4
  • build *
  • cmake >=3.28
  • flake8 >=3.7.7
  • furo *
  • importlib_metadata *
  • mpi4py >=3.0.3
  • networkx >=2.0
  • numpy >1.7
  • packaging *
  • pip >=10.1
  • pybind11 >=2.12
  • pytest >=4.6
  • setuptools >=42
  • sphinx-copybutton *
  • sphinx_inline_tabs *
  • sphinxcontrib-plantuml >=0.14
  • wheel *