Molly

Molecular simulation in Julia

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 2 DOI reference(s) in README
○
Academic publication links
✓
Committers with academic emails
1 of 29 committers (3.4%) from academic institutions
○
Institutional organization owner
○
JOSS paper metadata
○
Scientific vocabulary similarity
Low similarity (13.7%) to scientific vocabulary

Keywords

julia lennard-jones molecular-dynamics molecular-simulation physics-simulation protein-structure structural-bioinformatics

Keywords from Contributors

pde interpretability matrix-exponential standards physics julialang meshing julia-package hack research

Last synced: 4 months ago · JSON representation ·

Repository

Molecular simulation in Julia

Basic Info

Host: GitHub
Owner: JuliaMolSim
License: other
Language: Julia
Default Branch: master
Homepage:
Size: 90.8 MB

Statistics

Stars: 444
Watchers: 19
Forks: 58
Open Issues: 13
Releases: 41

Topics

julia lennard-jones molecular-dynamics molecular-simulation physics-simulation protein-structure structural-bioinformatics

Created over 7 years ago · Last pushed 5 months ago

Metadata Files

Readme Changelog License Code of conduct Citation

Much of science can be explained by the movement and interaction of molecules. Molecular dynamics (MD) is a computational technique used to explore these phenomena, from noble gases to biological macromolecules. Molly.jl is a pure Julia package for MD, and for the simulation of physical systems more broadly.

The package is described in a talk at JuliaCon 2024, an earlier talk at Enzyme Conference 2023 and a tutorial at the MolSSI JuliaMolSim Workshop 2024. Slides are also available for a tutorial in September 2023.

Implemented features include: - Non-bonded interactions - Lennard-Jones Van der Waals/repulsion force, electrostatic Coulomb potential and reaction field, gravitational potential, soft sphere potential, Mie potential, Buckingham potential, soft core variants. - Bonded interactions - harmonic and Morse bonds, bond angles, torsion angles, harmonic position restraints, FENE bonds. - Interface to allow definition of new interactions, simulators, thermostats, neighbor finders, loggers etc. - Read in OpenMM force field files and coordinate files supported by Chemfiles.jl. There is also experimental support for Gromacs files. - Write out trajectory files in formats supported by Chemfiles.jl, including DCD and XTC. - Verlet, velocity Verlet, Störmer-Verlet, flexible Langevin and Nosé-Hoover integrators. - Andersen, Berendsen and velocity rescaling thermostats. - Monte Carlo barostat and variants. - Steepest descent energy minimization. - Replica exchange molecular dynamics. - Monte Carlo simulation. - Periodic, triclinic and infinite boundary conditions. - Constraints with SHAKE and RATTLE - Flexible loggers to track arbitrary properties throughout simulations. - Cutoff algorithms for non-bonded interactions. - Various neighbor list implementations to speed up the calculation of non-bonded forces, including the use of CellListMap.jl. - Implicit solvent GBSA methods. - Unitful.jl compatibility so numbers have physical meaning. - Set up crystal systems using SimpleCrystals.jl. - Automatic multithreading. - GPU acceleration on all backends supported by KernelAbstractions.jl, with better performance on CUDA-enabled devices. - Run with Float64, Float32 or other float types. - Some analysis functions, e.g. RDF. - Visualise simulations as animations with Makie.jl. - Compatibility with AtomsBase.jl and AtomsCalculators.jl. - Interface to use Python ASE calculators. - Control of random numbers during simulation, allowing reproducible stochastic simulations. - Differentiable molecular simulation. This is a unique feature of the package and the focus of its current development.

Features not yet implemented include: - High GPU performance. - Ewald or particle mesh Ewald summation. - Full support for constrained bonds and angles. - Protein preparation - solvent box, add hydrogens etc. - Simulators such as metadynamics. - Quantum mechanical modelling. - Domain decomposition algorithms. - Alchemical free energy calculations. - High test coverage. - API stability.

Installation

Julia is required, with Julia v1.10 or later required to get the latest version of Molly. It is recommended to run on the current stable Julia release for the best performance. Install Molly from the Julia REPL. Enter the package mode by pressing ] and run add Molly.

Usage

Some examples are given here, see the documentation for more on how to use the package.

Simulation of a Lennard-Jones fluid: ```julia using Molly

natoms = 100 boundary = CubicBoundary(2.0u"nm") temp = 298.0u"K" atommass = 10.0u"g/mol"

atoms = [Atom(mass=atommass, σ=0.3u"nm", ϵ=0.2u"kJ * mol^-1") for i in 1:natoms] coords = placeatoms(natoms, boundary; mindist=0.3u"nm") velocities = [randomvelocity(atommass, temp) for i in 1:natoms] pairwise_inters = (LennardJones(),) simulator = VelocityVerlet( dt=0.002u"ps", coupling=AndersenThermostat(temp, 1.0u"ps"), )

sys = System( atoms=atoms, coords=coords, boundary=boundary, velocities=velocities, pairwiseinters=pairwiseinters, loggers=(temp=TemperatureLogger(100),), )

simulate!(sys, simulator, 10_000) ```

Simulation of a protein: ```julia using Molly

sys = System( joinpath(dirname(pathof(Molly)), "..", "data", "5XER", "gmxcoords.gro"), joinpath(dirname(pathof(Molly)), "..", "data", "5XER", "gmxtopff.top"); nonbondedmethod="pme", loggers=( temp=TemperatureLogger(10), writer=TrajectoryWriter(10, "traj5XER1ps.pdb"), ), )

temp = 298.0u"K" random_velocities!(sys, temp) simulator = VelocityVerlet( dt=0.0002u"ps", coupling=AndersenThermostat(temp, 1.0u"ps"), )

simulate!(sys, simulator, 5_000) ```

The above 1 ps simulation looks something like this when you view it in VMD: MD simulation

Contributing

Contributions are very welcome including reporting bugs, fixing bugs, adding new features, improving performance, adding tests and improving documentation. Feel free to open an issue or use the channels below to discuss your contribution. New features will generally require tests to be added as well. See the roadmap issue for some discussion of recent progress and future plans.

Join the #juliamolsim channel on the Julia Slack, the #molly channel on the JuliaMolSim Zulip or post on the Julia Discourse to discuss the usage and development of Molly.jl.

Molly.jl follows the Contributor Covenant code of conduct.

Citation

If you use Molly, please cite the following paper (bib entry here):

Greener JG. Differentiable simulation to develop molecular dynamics force fields for disordered proteins, Chemical Science 15, 4897-4909 (2024)

A paper involving more contributors with further details on the software will be written at some point.

Interested?

There is the possibility of a postdoc position involving the development and use of Molly. Contact Joe Greener with informal enquiries.

Owner

Name: Molecular Simulation in Julia
Login: JuliaMolSim
Kind: organization

Repositories: 13
Profile: https://github.com/JuliaMolSim

Citation (CITATION.bib)

@article{Greener2024,
    author = "Greener, Joe G",
    title = "{Differentiable simulation to develop molecular dynamics force fields for disordered proteins}",
    journal = "Chemical Science",
    year = "2024",
    volume = "15",
    pages = "4897-4909",
    url = "https://doi.org/10.1039/D3SC05230C",
}

GitHub Events

Total

Fork event: 5
Create event: 15
Commit comment event: 8
Release event: 3
Issues event: 13
Watch event: 42
Delete event: 14
Member event: 3
Issue comment event: 126
Push event: 167
Pull request review event: 19
Pull request review comment event: 34
Pull request event: 34

Last Year

Fork event: 5
Create event: 15
Commit comment event: 8
Release event: 3
Issues event: 13
Watch event: 42
Delete event: 14
Member event: 3
Issue comment event: 126
Push event: 167
Pull request review event: 19
Pull request review comment event: 34
Pull request event: 34

Committers

Last synced: 8 months ago

All Time

Total Commits: 1,869
Total Committers: 29
Avg Commits per committer: 64.448
Development Distribution Score (DDS): 0.259

Past Year

Commits: 237
Committers: 6
Avg Commits per committer: 39.5
Development Distribution Score (DDS): 0.143

Top Committers

Name	Email	Commits
Joe Greener	j**r@h**k	1,384
ejmeitz	5****z	137
Jaydev Singh Rao	5****R	103
Noé Blassel	n**l@g**m	64
Sebastian Micluța-Câmpeanu	m**5@g**m	48
chemicalfiend	t**1@g**m	23
Leandro Martinez	l**o@i**r	19
Peppone98	g**9@g**m	17
Diego Ugarte	d**e@o**m	14
James Schloss	j**s@g**m	12
ywitzky	1****y	8
Yusheng Zhao	y**0@o**m	8
github-actions[bot]	4****]	5
Sikorski	s**i@z**e	4
Ehsan	e**n@d**4	3
CompatHelper Julia	c**y@j**g	3
Maximilian Scheurer	m**r@m**m	2
Ruibin Liu	r**8@g**m	2
dependabot[bot]	4****]	2
longemen3000	l**0@g**m	2
ederag	e**a@g**r	1
Teemu Järvinen	t**n@g**m	1
Lee, Dohyeon	d**8@k**r	1
Jeremiah DeGreeff	d**f@m**u	1
Hiroharu Sugawara	h**a@g**m	1
Ellipse0934	a**7@g**m	1
Alessio Parato	a**o@M**l	1
Ehsan	e**i@p**m	1
Alexander Seiler	s**x@g**m	1

Committer Domains (Top 20 + Academic)

mit.edu: 1 kaist.ac.kr: 1 gmx.fr: 1 me.com: 1 julialang.org: 1 zib.de: 1 iqm.unicamp.br: 1 hotmail.co.uk: 1

Issues and Pull Requests

Last synced: 4 months ago

All Time

Total issues: 62
Total pull requests: 131
Average time to close issues: 7 months
Average time to close pull requests: about 1 month
Total issue authors: 37
Total pull request authors: 26
Average comments per issue: 4.69
Average comments per pull request: 4.6
Merged pull requests: 84
Bot issues: 0
Bot pull requests: 44

Past Year

Issues: 5
Pull requests: 27
Average time to close issues: 3 days
Average time to close pull requests: 12 days
Issue authors: 5
Pull request authors: 6
Average comments per issue: 6.8
Average comments per pull request: 1.85
Merged pull requests: 16
Bot issues: 0
Bot pull requests: 15

View more stats

Top Authors

Issue Authors

ejmeitz (6)
SebastianM-C (4)
jgreener64 (4)
JaydevSR (4)
HLinde (3)
jrdegreeff (3)
axsk (3)
jty-computation (2)
leios (2)
nwalet (2)
bondrewd (2)
SoDantas8452 (1)
Nick-Mul (1)
skycolt (1)
moradza (1)

Pull Request Authors

github-actions[bot] (50)
ejmeitz (26)
JaydevSR (12)
dependabot[bot] (11)
noeblassel (9)
chemicalfiend (6)
leios (6)
bondrewd (5)
lmiq (4)
Ruibin-Liu (3)
jgreener64 (3)
axsk (3)
ywitzky (2)
tjjarvinen (2)
Omar-Elrefaei (2)

Top Labels

Issue Labels

good first issue (1) discussion (1)

Pull Request Labels

dependencies (11) github_actions (1)

Packages

Total packages: 3
Total downloads:
- julia 19 total

Total dependent packages: 1
(may contain duplicates)
Total dependent repositories: 0
(may contain duplicates)
Total versions: 123

proxy.golang.org: github.com/JuliaMolSim/Molly.jl

Documentation: https://pkg.go.dev/github.com/JuliaMolSim/Molly.jl#section-documentation
License: other
Latest release: v0.22.3
published 6 months ago

Versions: 41
Dependent Packages: 0
Dependent Repositories: 0

Rankings

Dependent packages count: 5.4%

Average: 5.6%

Dependent repos count: 5.8%

Last synced: 5 months ago

proxy.golang.org: github.com/juliamolsim/molly.jl

Documentation: https://pkg.go.dev/github.com/juliamolsim/molly.jl#section-documentation
License: other
Latest release: v0.22.3
published 6 months ago

Versions: 41
Dependent Packages: 0
Dependent Repositories: 0

Rankings

Dependent packages count: 5.4%

Average: 5.6%

Dependent repos count: 5.8%

Last synced: 5 months ago

juliahub.com: Molly

Molecular simulation in Julia

Documentation: https://docs.juliahub.com/General/Molly/stable/
License: MIT
Latest release: 0.22.3
published 7 months ago

Versions: 41
Dependent Packages: 1
Dependent Repositories: 0
Downloads: 19 Total

Rankings

Stargazers count: 2.8%

Forks count: 3.4%

Average: 9.8%

Dependent repos count: 9.9%

Dependent packages count: 23.0%

Last synced: 5 months ago

Dependencies

.github/workflows/CI.yml actions

actions/cache v1 composite
actions/checkout v2 composite
codecov/codecov-action v1 composite
julia-actions/julia-buildpkg v1 composite
julia-actions/julia-processcoverage v1 composite
julia-actions/julia-runtest v1 composite
julia-actions/setup-julia v1 composite

.github/workflows/CompatHelper.yml actions

Molly

Science Score: 67.0%

Keywords

Keywords from Contributors

Repository

Basic Info

Statistics

Topics

Metadata Files

README.md

Installation

Usage

Contributing

Citation

Interested?

Owner

Citation (CITATION.bib)

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Packages

proxy.golang.org: github.com/JuliaMolSim/Molly.jl

Rankings

proxy.golang.org: github.com/juliamolsim/molly.jl

Rankings

juliahub.com: Molly

Rankings

Dependencies