ewald-splitting-with-prolates
Science Score: 67.0%
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Low similarity (18.4%) to scientific vocabulary
Last synced: 6 months ago
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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
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- given-names: Brian
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- given-names: Vladimir
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orcid: "https://orcid.org/0009-0008-3889-3891"
- given-names: Paul
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orcid: "https://orcid.org/0000-0002-2268-0065"
- given-names: Hugh
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- given-names: Eliane
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orcid: "https://orcid.org/0000-0002-5875-6682"
- given-names: Ania
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- given-names: Mahesh
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- given-names: Giacomo
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- given-names: Stefan
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- 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
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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
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- given-names: Justin A.
family-names: Lemkul
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- given-names: Magnus
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family-names: Merz
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- 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
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- lu1and10 (1)
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