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<!doctype html>
<html class="no-js" lang="">
<head>
<meta charset="utf-8">
<title>MoSDeF</title>
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<main id="main" style="position: relative;">
<div class="section no-pad-bot banner-background">
<div class="row center">
<h3 class="white-text"> Molecular Simulation Design Framework (MoSDeF)</h3>
<p class="subtitle white-text">
MoSDeF presents a set of extensible Python tools designed to facilitate the initialization,
<br> atom-typing, and screening of soft matter systems using molecular simulation.
</p>
<div class="row center">
<a id="get-started-btn" class="btn-large waves-effect waves-light orange darken-1">Get
Started!</a>
</div>
</div>
</div>
<div class="container">
<div class="section">
<div class="row">
<h7 class="black-text">
The MoSDeF tools have been designed to facilitate the hierarchical construction of both atomistic
and coarse-grained system configurations, the application of classical force fields (i.e.,
atom-typing),
encapsulation of chemical topology information, and the generation of input files for a variety of
molecular dynamics and Monte Carlo simulation engines, including LAMMPS, GROMACS, HOOMD-Blue,
Cassandra, and GOMC.
</h7>
</div>
<div class="row center">
<div class="col s12 l8">
<div id="slides-container" class="hide-on-med-and-down">
<div id="mosdefSlides" class="carousel carousel-slider" data-indicators="true">
<a href="#one!" class="carousel-item"><img src="images/slides/0001.jpg"></a>
<a href="#two!" class="carousel-item"><img src="images/slides/0002.jpg"></a>
<a href="#three!" class="carousel-item"><img src="images/slides/0003.jpg"></a>
<a href="#four!" class="carousel-item"><img src="images/slides/0004.jpg"></a>
<a href="#five!" class="carousel-item"><img src="images/slides/0005.jpg"></a>
<a href="#six!" class="carousel-item"><img src="images/slides/0006.jpg"></a>
<a href="#seven!" class="carousel-item"><img src="images/slides/0007.jpg"></a>
<a href="#!eight" class="carousel-item"><img src="images/slides/0008.jpg"></a>
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</div>
</div>
</div>
<div class="col s12 l4">
<img src="./images/slideshow.png" style="max-width: 100%;margin-top: 10%"
alt="mosdef-slideshow"/>
</div>
</div>
</div>
<div class="divider"></div>
<div class="section">
<div class="row" style="text-align: justify;">
<div class="col s12 l4">
<h4>TRUE Simulations</h4>
<p class="text-justify">
Through the MoSDeF integrated framework, the exact procedures used to set up and perform
simulation workflows and associated metadata (i.e. the provenance) can be scripted,
encapsulated, version-controlled, preserved, and later reproduced by other researchers. This
allows molecular simulation studies to be conducted and published in a manner that is <b>TRUE
</b>: “<b>Transparent</b>, <b>Reproducible</b>, <b>Usable by others</b>, and <b>Extensible
</b>.” The following <a
href="https://www.tandfonline.com/doi/full/10.1080/00268976.2020.1742938"
target="_blank">paper</a> highlights these principles in details.
</p>
<div class="center-align">
<img style="max-width: 100%" src="images/TRUESIMS.png" alt="True Simulations"/>
</div>
</div>
<div class="col s12 l4">
<h4>Flexibility</h4>
<p class="text-justify">
System construction and initialization are performed in a simulation engine agnostic fashion,
allowing users to use a single set of scripts to generate inputs for a variety of different
simulation engines.
<br>
Because systems are constructed in a hierarchical, scriptable fashion, modifications to system
chemistry can be easily made, allowing for screening over chemical space.
</p>
<div class="hide-on-med-and-down">
<br>
</div>
<div class="center-align">
<img style="max-width: 100%;" src="images/flexibility.png"
alt="Flexibility"/>
</div>
</div>
<div class="col s12 l4">
<h4>Community</h4>
<p class="text-justify">
MoSDeF is designed to allow system construction scripts to be easily made into easy to
distribute libraries; similarly, forcefield files contain parameters and their usage rules that
can be easily shared and version controlled.
</p>
<a href="https://groups.google.com/g/mosdef-users"
target="_blank"><h6>Join the mailing list</h6></a>
<a href="https://gitter.im/mosdef-hub/Lobby" target="_blank"><h6>Mosdef Gitter </h6></a>
<a href="https://github.com/mosdef-hub" target="_blank"><h6>Github Organization</h6></a>
<div class="hide-on-med-and-down">
<br>
</div>
<div class="center-align">
<img src="images/community.png" style="max-width: 100%" alt="community"/>
</div>
</div>
</div>
</div>
<div class="divider"></div>
<div class="section">
<div class="row">
<div class="col l6 m12 s12">
<h4 id="ecoSystem" class="col s12 light header center">Quick Start</h4>
<h7 class="black-text">
The easiest way to get started with <b>MoSDeF</b> is to go through our tutorials. Below is a
curated list of quick start guides:
</h7>
<table class="striped">
<thead>
<tr>
<th>Details</th>
<th style="text-align: center">GitHub</th>
<th style="text-align: center">Binder</th>
</tr>
</thead>
<tbody>
<tr>
<td><b>MosDeF Tutorials</b>: Curated tutorials for the MosDeF Framework</td>
<td style="text-align: center"><a class="black-text"
href="https://github.com/mosdef-hub/mosdef_tutorials"
target="_blank">
<i class="fa fa-github fa-2x"></i></a></td>
<td style="text-align: center"><a target="_blank"
href="https://mybinder.org/v2/gh/mosdef-hub/mbuild_tutorials/master"
rel="nofollow">
<img src="https://camo.githubusercontent.com/aa6359bb47ca71509b05d2981fc5c878ab6a6601fe88445c375c3f0a7e20e36d/68747470733a2f2f6d7962696e6465722e6f72672f62616467652e737667"
alt="Binder" data-canonical-src="https://mybinder.org/badge.svg"
style="max-width: 100%;"></a></td>
</tr>
<tr>
<td><b>mBuild Tutorials</b>: Curated tutorials for mBuild</td>
<td style="text-align: center"><a class="black-text"
href="https://github.com/mosdef-hub/mbuild_tutorials"
target="_blank">
<i class="fa fa-github fa-2x"></i></a></td>
<td style="text-align: center"><a target="_blank"
href="https://mybinder.org/v2/gh/mosdef-hub/mbuild_tutorials/master"
rel="nofollow">
<img src="https://camo.githubusercontent.com/aa6359bb47ca71509b05d2981fc5c878ab6a6601fe88445c375c3f0a7e20e36d/68747470733a2f2f6d7962696e6465722e6f72672f62616467652e737667"
alt="Binder" data-canonical-src="https://mybinder.org/badge.svg"
style="max-width: 100%;"></a></td>
</tr>
<tr>
<td><b>Foyer Tutorials</b>: Curated tutorials for Foyer</td>
<td style="text-align: center"><a class="black-text"
href="https://github.com/mosdef-hub/foyer_tutorials"
target="_blank"><i
class="fa fa-github fa-2x"></i></a></td>
<td style="text-align: center"><a target="_blank"
href="https://mybinder.org/v2/gh/mosdef-hub/foyer_tutorials/master"
rel="nofollow">
<img src="https://camo.githubusercontent.com/aa6359bb47ca71509b05d2981fc5c878ab6a6601fe88445c375c3f0a7e20e36d/68747470733a2f2f6d7962696e6465722e6f72672f62616467652e737667"
alt="Binder" data-canonical-src="https://mybinder.org/badge.svg"
style="max-width: 100%;"></a></td>
</tr>
</tbody>
</table>
</div>
<div class="col l5 m12 s12 offset-l1 left-align">
<h4 class="col s12 light header center">Quick Peek</h4>
<div>
<img class="responsive-img" src="images/mosdef-glance.png"/>
</div>
</div>
</div>
</div>
<div class="divider"></div>
<div class="section">
<div class="row center">
<h4 class="col s12 light header center">Foundational MoSDeF Repositories</h4>
</div>
<div class="row">
<div class="col s12 l4">
<div class="card small banner-background">
<div class="card-content white-text">
<div class="card-title">mBuild</div>
<p>A hierarchical, component based molecule builder</p>
<span style="position: absolute; top: 2%; right: 2%; border: 2%;"
class="circle black valign-wrapper"><i
class="material-icons lime-text accent-3">star</i></span>
<a style="margin-right:15%" class="btn-floating halfway-fab waves-effect waves-light black"
href=https://mbuild.mosdef.org target="_blank"><i
class="material-icons">more</i></a>
<a class="btn-floating halfway-fab waves-effect waves-light black"
href=https://github.com/mosdef-hub/mbuild target="_blank"><i
class="fa fa-github"></i></a>
</div>
</div>
</div>
<div class="col s12 l4">
<div class="card small banner-background">
<div class="card-content white-text">
<div class="card-title">Foyer</div>
<p>A package for atom-typing as well as applying and disseminating forcefields</p>
<span style="position: absolute; top: 2%; right: 2%; border: 2%;"
class="circle black valign-wrapper"><i
class="material-icons lime-text accent-3">star</i></span>
<a style="margin-right:15%" class="btn-floating halfway-fab waves-effect waves-light black"
href=https://foyer.mosdef.org target="_blank"><i
class="material-icons">more</i></a>
<a class="btn-floating halfway-fab waves-effect waves-light black"
href=https://github.com/mosdef-hub/foyer target="_blank"><i class="fa fa-github"></i></a>
</div>
</div>
</div>
<div class="col s12 l4">
<div class="card small banner-background">
<div class="card-content white-text">
<div class="card-title">GMSO</div>
<p>Flexible storage of chemical topology for molecular simulation</p>
<span style="position: absolute; top: 2%; right: 2%; border: 2%;"
class="circle black valign-wrapper"><i
class="material-icons lime-text accent-3">star</i></span>
<a style="margin-right:15%" class="btn-floating halfway-fab waves-effect waves-light black"
href=https://gmso.mosdef.org target="_blank"><i
class="material-icons">more</i></a>
<a class="btn-floating halfway-fab waves-effect waves-light black"
href=https://github.com/mosdef-hub/gmso target="_blank"><i class="fa fa-github"></i></a>
</div>
</div>
</div>
</div>
</div>
<div class="divider"></div>
<div class="section">
<div class="row" style="text-align: justify;">
<div class="col s12 l6">
<h5>Other MoSDeF Projects</h5>
<div class="collection">
<div class="collection-item"><a href="https://github.com/mosdef-hub/forcefield_template"
target="_blank"><b>Forcefield Template</b></a>: A template repo
for disseminating force
fields with foyer
</div>
<div class="collection-item"><a href="https://github.com/mosdef-hub/nanoparticle_optimization"
target="_blank"><b>Nanoparticle Optimization</b></a>: Deriving
potentials for
coarse-grained nanoparticles via potential-matching
</div>
<div class="collection-item"><a href="https://github.com/mosdef-hub/msibi"
target="_blank"><b>MultiState Boltzmann Inversion
(MS-IBI)</b></a>: Manage and run pair
potential optimizations using multistate iterative Boltzmann inversion
</div>
<div class="collection-item"><a href="https://github.com/mosdef-hub/mosdef_tutorials"
target="_blank"><b>MoSDeF Tutorials</b></a>: A set of tutorials
to introduce new users to the MoSDeF (Molecular Simulation Design Framework) toolkit
</div>
<div class="collection-item"><a href="https://github.com/mosdef-hub/mbuild_tutorials"
target="_blank"><b>mBuild Tutorials</b></a>: A set of tutorials
to introduce new users to
mBuild
</div>
<div class="collection-item"><a href="https://github.com/mosdef-hub/foyer_tutorials"
target="_blank"><b>foyer Tutorials</b></a>: A set of tutorials
to introduce new users to
foyer
</div>
</div>
</div>
<div class="col s12 l6">
<h5>Projects Using MoSDeF</h5>
<div class="collection">
<div class="collection-item"><a href="https://github.com/MaginnGroup/mosdef_cassandra"
target="_blank"><b>MoSDeF
Cassandra</b></a>:
MoSDeF compatible wrapper for Cassandra Monte Carlo code
</div>
<div class="collection-item"><a href="https://github.com/GOMC-WSU/MoSDeF-GOMC"
target="_blank"><b>MoSDeF GOMC</b></a>:
MoSDeF compatible wrapper for GPU Optimized Monte Carlo (GOMC) code
</div>
<div class="collection-item"><a href="https://github.com/cmelab/planckton" target="_blank"><b>
planckton</b></a>: Reproducible
exploration of organic photovoltaic morphology self-assembly using molecular dynamics.
</div>
<div class="collection-item">
<a href="https://github.com/colinebunner/MoSDeF-CP2K-Writer"
target="_blank"><b>MosDeF-CP2K-Writer</b></a>: Scripted control and better documentation
of CP2K simulations in accord with the goals of the CSSI MoSDeF project
</div>
<div class="collection-item"><a href="https://github.com/mosdef-hub/gmso_showcase"
target="_blank"><b>GMSO Showcase</b></a>: Interactive
demo/tutorial of current GMSO features
and design decisions.
</div>
<div class="collection-item"><a href="https://github.com/cmelab/grits"
target="_blank"><b>GRiTS</b></a>: GRiTS Reduces/Restores
Topology with SMILES
</div>
<div class="collection-item"><a href="https://github.com/mosdef-hub/mosdef-workflows"
target="_blank"><b>MoSDeF Workflows</b></a>: Sample molecular
simulation workflows using
MoSDeF
</div>
</div>
</div>
</div>
<p class="black-text">Also, checkout projects from our collaborators:
<a href="https://github.com/cmelab" target="_blank">Boise State</a> |
<a href="https://github.com/glotzerlab" target="_blank">Michigan</a> |
<a href="https://github.com/MaginnGroup" target="_blank">Notre Dame</a> |
<a href="https://github.com/GOMC-WSU" target="_blank">Wayne State</a>.
</p>
</div>
<div class="divider"></div>
<div class="section">
<div class="row center">
<h4 class="col s12 light header center">Collaborators</h4>
</div>
<div class="row center">
<p class="flow-text"><br/> MoSDeF is supported by a Cyberinfrastructure for Sustained Scientific
Innovation (CSSI) grant funded by the National Science Foundation Office of Advanced
Cyberinfrastructure.</p>
</div>
<div id="colabUniversities" class="row center carousel">
<div class="card carousel-item hoverable colab-universities col s8 m4 l3 center">
<a href="https://vanderbilt.edu/" alt="Vanderbilt University" target="_blank">
<img src="images/Vanderbilt_University_logo.svg" alt="Vandy">
</a>
<div class="card-content">
<a href="https://engineering.vanderbilt.edu/bio/peter-cummings" target="_blank">Peter T.
Cummings</a>,
<a href="https://www.nsf.gov/awardsearch/showAward?AWD_ID=1835874"
target="_blank">1835874</a>
</div>
</div>
<div class="card carousel-item hoverable colab-universities col s8 m4 l3 center">
<a href="https://vanderbilt.edu/" alt="Vanderbilt University" target="_blank">
<img src="images/Vanderbilt_University_logo.svg" alt="Vandy">
</a>
<div class="card-content">
<a href="https://engineering.vanderbilt.edu/bio/clare-mccabe" target="_blank">Clare
M<sup>c</sup>Cabe</a>,
<a href="https://www.nsf.gov/awardsearch/showAward?AWD_ID=1835874"
target="_blank">1835874</a>
</div>
</div>
<div class="card carousel-item hoverable colab-universities col s8 m4 l3 center">
<a href="https://vanderbilt.edu/" alt="Vanderbilt University" target="_blank">
<img src="images/Vanderbilt_University_logo.svg" alt="Vandy">
</a>
<div class="card-content">
<a href="https://engineering.vanderbilt.edu/bio/akos-ledeczi" target="_blank">Akos
Ledeczi</a>,
<a href="https://www.nsf.gov/awardsearch/showAward?AWD_ID=1835874"
target="_blank">1835874</a>
</div>
</div>
<div class="card carousel-item colab-universities col s8 m4 l3 center">
<a href="https://boisestate.edu/" alt="Boise State University" target="_blank">
<img src="images/Boise_State_University_logo.svg" alt="boise">
</a>
<div class="card-content">
<a href="https://www.boisestate.edu/coen-materials/faculty-and-staff/eric-jankowski-ph-d/"
target="_blank">Eric Jankowski</a>,
<a href="https://www.nsf.gov/awardsearch/showAward?AWD_ID=1835593"
target="_blank">1835593</a>
</div>
</div>
<div class="card carousel-item colab-universities col s8 m4 l3 center">
<a href="https://udel.edu/" alt="University of Delaware" target="_blank">
<img src="images/University_of_Delaware_wordmark.svg" alt="delaware">
</a>
<div class="card-content">
<a href="https://cbe.udel.edu/people/faculty/arthij/" target="_blank">Arthi Jayaraman</a>,
<a href="https://www.nsf.gov/awardsearch/showAward?AWD_ID=1835613"
target="_blank">1835613</a>
</div>
</div>
<div class="card carousel-item colab-universities col s8 m4 l3 center">
<a href="https://uh.edu/" alt="University of Houston" target="_blank">
<img src="images/University_of_Houston_logo.svg" alt="houston">
</a>
<div class="card-content">
<a href="http://www.chee.uh.edu/faculty/palmer" target="_blank">Jeremy Palmer</a>,
<a href="https://www.nsf.gov/awardsearch/showAward?AWD_ID=1835560"
target="_blank">1835560</a>
</div>
</div>
<div class="card carousel-item colab-universities col s8 m4 l3 center">
<a href="https://umich.edu/" alt="University of Michigan" target="_blank">
<img src="images/University_of_Michigan_logo.svg" alt="michigan">
</a>
<div class="card-content">
<a href="https://che.engin.umich.edu/people/sharon-glotzer/" target="_blank">Sharon
C. Glotzer</a>,
<a href="https://www.nsf.gov/awardsearch/showAward?AWD_ID=1835612"
target="_blank">1835612</a>
</div>
</div>
<div class="card carousel-item colab-universities col s8 m4 l3 center">
<a href="https://umn.edu/" alt="University of Minessota" target="_blank">
<img src="images/University_of_Minnesota.svg" alt="minessota">
</a>
<div class="card-content">
<a href="http://siepmann.chem.umn.edu/people/research-director" target="_blank">Joern
Ilja. Siepmann</a>,
<a href="https://www.nsf.gov/awardsearch/showAward?AWD_ID=1835067"
target="_blank">1835067</a>
</div>
</div>
<div class="card carousel-item colab-universities col s8 m3 l3 center">
<a href="https://nd.edu/" alt="University of Notre Dame" target="_blank">
<img src="images/University_of_Notre_Dame_logo.svg" alt="notredame">
</a>
<div class="card-content">
<a href="https://engineering.nd.edu/profiles/emaginn" target="_blank">Edward J.
Maginn</a>,
<a href="https://www.nsf.gov/awardsearch/showAward?AWD_ID=1835630"
target="_blank">1835630</a>
</div>
</div>
<div class="card carousel-item colab-universities col s8 m3 l3 center">
<a href="https://wayne.edu/" alt="Wayne State University" target="_blank">
<img src="images/Wayne_State_University_logo.svg" alt="wayne">
</a>
<div class="card-content">
<a href="https://engineering.wayne.edu/profile/ai8111" target="_blank">Jeffrey J.
Potoff</a>,
<a href="https://www.nsf.gov/awardsearch/showAward?AWD_ID=1835713"
target="_blank">1835713</a>
</div>
</div>
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