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atomes: Analysis, visualization, edition and
post-processing of 3D atomic scale models

Sébastien Le Roux

► To cite this version:

Sébastien Le Roux. atomes: Analysis, visualization, edition and post-processing of 3D atomic scale models. Computational Materials Science, 2025, 253, pp.113805. 10.1016/j.commatsci.2025.113805. hal-05028755

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Distributed under a Creative Commons Attribution 4.0 International License
**atomes**: analysis, visualization, edition and post-processing of 3D
atomic scale models

Sébastien Le Roux, ORCID: 0000-0002-1912-6960

Institut de Physique et Chimie des Matériaux de Strasbourg, Université de Strasbourg, CNRS UMR 7504, 23 rue de Loess, BP
43, F-67034 Strasbourg Cedex 2, France

**Abstract**

**atomes** is a cross-platform open source program developed to analyze, to visualize and to edit/create large three-dimensional atomic scale models. By regrouping advanced analysis techniques, 3D visualization and 3D edition, **atomes** introduces innovative 3D rendering possibilities and intuitive applications of the calculation results. **atomes** also provides an advanced input preparation system for further calculations using well known classical, *ab-initio* and QM-MM molecular dynamics codes. To prepare the input files for these calculations is likely to be the key, and most complicated step towards MD simulations. **atomes** offers a user-friendly assistant to help and guide the user step by step to achieve this crucial step.

Email address: sebastien.leroux@ipcms.unistra.fr (Sébastien Le Roux, ORCID: 0000-0002-1912-6960)
<figure><img src="image_3.png" /><figcaption>Figure 1: Visual overview of the *atomes* program.</figcaption></figure>

# 1. Introduction

From biological systems to periodic structures, or isolated molecules, detailed knowledge about the three-dimensional (3D) atomic scale organisation is a prerequisite to understand and predict the properties of materials. However on an experimental point of view the precise atomic scale structure often remains elusive, in which case scientists have to rely on computers in order to gain insight on that information.

Several approaches can be envisioned to study materials using theoretical methodologies and the corresponding computational tools. But overall the procedure is similar and can be briefly schematized in the 3 following steps:

1. Creating an initial model: building an initial atomic 3D structure, that does not necessarily have physical meaning.

2. Realising a numerical experiment: applying a physico-chemical model to the initial structure using
molecular simulation (Reverse Monte-Carlo, Monte-Carlo, Molecular Dynamics, etc.).

### 3. Analyzing the final model: evaluating and studying its physico-chemical properties.

Over the years many programs have been developed from open source software with various and uneven capabilities (VMD[1], Ovito[2], Avogadro[3], VESTA[4], Jmol[5], etc.) usually focusing on a particular step, to advanced and usually very expensive proprietary software (BIOVIA Material Studio[6], Schrödinger[7], Samson Connect[8], Molecular Operating Environment[9]) which tend to encompass the entire work procedure.

In this article we introduce a new and open source program, **atomes**, a computational material science tool box regrouping a comprehensive panel of specialized edition tools, several assistants dedicated to the preparation of numerical experiments, and, a large number of physico-chemical analysis. Advanced visualization utilities and capabilities being available at each stage of the process **atomes** introduces innovative 3D rendering possibilities and intuitive applications of the calculation results.

Importantly **atomes** is designed to analyze, to visualize and to create/edit large three-dimensional atomic scale models, and can handle MD trajectories from hundreds of thousands, up to millions, of atoms. Using OpenMP parallelization, file processing, coordination and physico-chemical analysis make use of the advantages of modern CPUs and their multiple cores. Consequently when importing atomic coordinates several properties are analyzed on the fly regardless of the size, in number of atoms or MD steps, and the periodicity of the system (see Sec. 4.2). Overall no other Free open source software regroups as many capabilities for analyzing (see Sec. 4.1), rendering (see Sec. 4.2), and editing atomic scale models (see Sec.4.3), and in such a comprehensive and user-friendly manner than **atomes**, several of these tools becoming for the time available as a Free Open Source software.

Furthermore **atomes** also provides an advanced input preparation system for further calculations using well known molecular dynamics codes: DL-POLY [10], LAMMPS [11], CPMD [12] and CP2K [13]. For classical molecular dynamics calculations **atomes** conveniently regroups most, if not all, free force fields parameters available to date [14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39] so that the creation of the force field can be first automated with the set of parameters selected by the user, and then if required entirely customized by the scientist.
## 2. Programming framework

**atomes** (Fig. 1) is developed in C, FORTRAN90 and GLSL (OpenGL shaders language). The GTK [40] API is used to create the **Graphical User Interface**, GTK3 (stable release) and GTK4 (beta) versions of the program being available.

The OpenMP [41] API for parallel programming is used to take advantage of the multiple cores of modern CPUs.

The 3D rendering is performed, via the ** taxa** widget, using modern OpenGL language [42], and
the **Epoxy** library is used to ensure the OpenGL function pointer management. Also the **FFmpeg** [43]
libraries (avutil, avformat, avcodec and swscale) are used to encode video from off-screen OpenGL
rendering.

2.1. Supported platforms

All dependencies of the program, from the GTK API for the GUI, to FFmpeg library for the video encoding where chosen because of their highly portable capabilities. These choices allow **atomes** to be a cross-platform software: Linux, MacOS and Windows versions of the program are available.

3. Overview

**atomes** allows to build, edit, study, analyze and compare multiple systems within the same instance
of the program. Each system, molecule, material, is defined in a data structure called **project**. **atomes**
projects files (*.apf) can be opened/saved separately, the list of opened project(s) appears in the left
side of the main window in a browsable tree-like structure. The entire list of project(s) displayed in this
part of the main window is a data structure called **workspace**, and **atomes** workspace files (*.awf) can
also be opened and saved, allowing to back-up the entire list of projects at once, preserving the possible
connections, data exchanges, between projects.

An illustration is presented in figure 1, many different projects being opened in the software's workspace.
To each of these project is assigned an OpenGL 3D window, few of them being visible in the overview
presented in figure 1.

**atomes** is designed to work on large atomic scale models, and can handle MD trajectories of million(s)
of atoms large systems. Models can be designed within the software itself but it is also possible to import
atomic coordinates in the following formats:

• XYZ [44] *

• Chem3D [45]

• CPMD trajectory [12] *

• VASP trajectory [46] *

• ISAACS Project File [47]

• PDB/ENT (Protein Data Bank) v3.30

• CIF (Crystallographic information)

• DL-POLY History file *

* including **NPT** trajectories (variable MD box parameters), that can therefore be visualized and analyzed using **atomes**.

**4. Features**

In this section we will briefly introduce some of the many capabilities offered by the **atomes** program.

**4.1. Analysis**

**atomes** can compute the following physico-chemical properties of 3D atomic scale models, from the
isolated molecule to the periodic system even with multiple unit cells (**NPT** trajectory):

• Radial distribution functions (RDFs) [48] including:

- Total $g(r)$, $G(r)$, $D(r)$, $T(r)$ for neutrons and X-rays

- Partial RDFs

- Bhatia-Thornton RDFs [49]

RDFs can be computed by i) direct real space calculation and/or ii) Fourier transforming of the
structure factor calculated using the Debye formalism [50]
* Structure factors $S(q)$ [50] including:

- Total $S(q)$ for neutrons and X-rays

- Total $Q(q)$ [50, 51] for neutrons and X-rays

- Partial $S(q)$:

* Faber-Ziman [52] partial $S(q)$

* Ashcroft-Langreth [53, 54, 55] partial $S(q)$

* Bhatia-Thornton [56] partial $S(q)$

Structure factors can be computed by i) Fourier transforming of the radial distribution functions and/or ii) using the Debye formalism [50]

* Interatomic bond properties

- Coordination numbers

- Atomic near neighbor distribution

- Fraction of links between tetrahedra

- Fraction of tetrahedral units

- Bond lengths distribution

* Distribution of bond angles

* Distribution of dihedral angles

* Ring statistics, according to several definitions:

- All closed paths (no rules)

- King's rings [57, 58]

- Guttman's rings [59]

- Primitive rings [60, 61] (or Irreducible [62])

- Strong rings [60, 61]
And including options to:

- search only for ABAB rings

- exclude rings with homopolar bonds (A-A or B-B) from the analysis

Ring statistics is presented according to the R.I.N.G.S. method [63].

* Chain statistics, including options to:

- search only for AAAA chains

- search only for ABAB chains

- exclude chains with homopolar bonds (A-A or B-B) from the analysis

- search only for 1-(2)$_{n}-1$ chains

* Spherical harmonics invariant, $Q_l$, as local atomic ordering symmetry identifiers [64]

- Average $Q_l$ for all chemical species and each coordination unit

* Mean Square Displacement of atoms (MSD)

- Atomic species MSD

- Directional MSD (x, y, z, xy, xz, yz)

- Drift of the center of mass

In **atomes** each of these calculations is parallelized in OpenMP to take advantage of the CPUs cores. Furthermore depending on the number of atoms in the model and the number of configurations, or MD steps, either the atoms or the configurations are distributed over the cores to ensure the analysis to be as fast as possible.

For most of these calculations, results can be presented in the form of a graph handled within the software itself. Indeed **atomes** offers an advanced graph visualization interface where, as illustrated in figure 2, one can customize the rendering, work on the representation, and add, remove, or even edit the data set(s).

Furthermore some of these calculations have direct applications in the 3D representation of the atomic scale model (see section 4.2).
<figure><img src="image_4.png" /><figcaption>**Figure 2:** Analysis in the **atomes** program: the example of I-GeSe, 3 models have been produced using different DFT functionals [65, 66], these models can be analyzed using **atomes**, results can be compared, edited, customized.</figcaption></figure>
<figure><img src="image_5.png" /><figcaption>**Figure 3:** The idea of clones in the **atomes** program illustrated using a liquid Ge<sub>2</sub>Se<sub>3</sub> model [67]: left side: clones are hidden, right side: clones are shown and appear as translucent atoms and bonds.</figcaption></figure>

## 4.2. Visualization

**atomes** offers all the standard tools that can be expected by the scientist to analyze visually any atomic scale model: stylization, measurements, custom labels, atom search engine, coordination polyhedra, and more.

Here are some innovative tools implemented in **atomes**:

* **Clones:** as an education tool for the case of periodic systems **atomes** uses the idea of clones, or replica images, of atoms linked via Periodic Boundary Conditions (PBC). As illustrated in figure 3 in such case extra atoms called clones can optionally be added to the model on the edges of the simulation box to illustrate the real length and orientation of the chemical bonds found by using the PBC.

* **Color maps:** atoms and polyhedra color maps can easily be fine-tuned in **atomes**, several bonding-based color maps are natively available (see figure 4): atomic species, (1) total coordinations, (2) partial coordinations, (3) molecular fragments (isolated objects), and (4) molecules (topological analysis), as well as classical MD force field numbering. The analysis required to access color maps (1) to (4) is performed on the fly when loading atomic coordinates, independently of the number of atoms and/or configurations in the system, or its periodicity.
<figure><img src="image_6.png" /><figcaption>**Figure 4:** Standard color maps in the **atomes** program, illustrated using Nickel phtalocyanine molecules (one H atom was removed from the molecule on top). From top to bottom: chemical species, total coordinations, partial coordinations, fragments (isolated objects) and molecules (topological analysis). Note that changing between color maps is really easy as simply pressing `a` is required.</figcaption></figure>

Alternatively it is also possible to read and use custom, user-defined, color map.

* **Environments dialog: atomes** offers an advanced configuration tool dedicated to the visual analysis of the structural units in the atomic scale model (coordination units, coordination polyhedra, rings, chains, fragments, molecules). As illustrated in figure 5 using this tool scientists can customize the rendering to highlight whatever unit or object that requires attention, furthermore that it can also be used to select atoms or objects for edition purposes.

* **Video encoding: atomes** offers real time encoding of the OpenGL window. Upon starting the
<figure><img src="image_7.png" /><figcaption>**Figure 5:** Some applications of the tools provided in the environments window in the **atomes** program, illustrated using a 3000 atoms gSiO₂ model. Top left: only Si(O₄) coordination units are shown. Top right: Si(O₄) tetrahedra are shown. Bottom right: all primitive rings of size 6, 8 and 10 atoms are shown. Bottom left: among King's rings only a single ring, the third ring of 20 atoms, is shown and the atoms selected.</figcaption></figure>
recording all actions performed by the user are stored. Then when stopping the recording, encoding becomes available and movies can be saved in different formats (MPEG, MP4, THEORA, H264, FLASH).

### 4.3. Edition

**atomes** regroups several tools that can help the scientist to design materials, including several standard edition features: molecular library, mouse edition (motion, rotation) of selected atoms or objects, box configuration tools (cell edition, add extra cells, adjust density ...).

**atomes** also provides a number of advanced and innovative tools:

* **Crystal builder:** **atomes**'s crystal builder allows to build structure, or super-structure using any of the 230 space groups. Not only atoms, but also molecular fragments can be used and inserted at crystalline positions to create the model. Furthermore, as illustrated in figure 6, it offers several possibilities to handle occupancy, and/or overlapping, so that it is possible to easily create crystalline structures with encapsulated molecules.

* **Surface creation and passivation:** **atomes** provides a tool to cut parallelepiped, cylindrical or spherical slabs into the material. Orientation, size, position and chemistry of the slab can be precisely controlled, and bridging atoms can be replaced by user defined objects (atoms or molecules) allowing to passivate the newly created surface, a illustration is provided in figure 7.

* **Advanced model edition window:** this tools allows to precisely move, remove, replace any atom(s) or group of atoms in the model. In each case the action can be performed either extremely precisely, or, completely randomly which is a way to generate defects and create disordered materials:
<figure><img src="image_8.png" /><figcaption>**Figure 6: Crystal builder in the atoms program: creating a diamond like, C₂₄₀ encapsulated toluene system.**</figcaption></figure>
<figure><img src="image_9.png" /><figcaption>**Figure 7:** Surface creation and passivation in a 3 million atoms disordered SiO₂ model: a spherical slab is created and non bridging O and Si atoms are passivated using respectively water molecules and S atoms.</figcaption></figure>
<figure><img src="image_10.png" /><figcaption>**Figure 8:** An example of model edition using **atomes**: first step substitution of all Cl atoms by water molecules (blue arrow), then random rotation of each water molecule independently (cyan arrow).</figcaption></figure>
### 4.4. Preparing MD calculations

Last but not least, **atomes** offers several input preparation assistants to setup further calculations with well known molecular dynamics codes:

* Classical MD: DL-POLY [10] and LAMMPS [11]

* ab-initio MD: CPMD [12] and CP2K [13]

* QM-MM MD (available soon): CPMD [12] and CP2K [13]

To prepare the input files for these calculations is likely to be the key, and most complicated step towards MD simulations. **atomes** offers a system of user-friendly assistant to help and guide the user step by step to achieve this crucial step.

In the case of classical MD calculations the complete set of parameters for a number of existing force fields have been made available:

* Amber: 94 [14], 96, 98 and 99 [15]

* CHARMM: 22 Proteins [16, 17], 22 Proteins and metals, 35 Ethers, 36 Carbohydrates [18, 19, 20, 21], 36 General [22, 23, 24, 25, 26], 36 Lipids [27], 36 Nucleid acids [28, 29], 36 Proteins [30], 36 Proteins and metals [31], Silicates [32]

* Consistent family of force fields: CVFF and CVFF Augmented [33, 34] CFF91 [35], PCFF [36] and COMPASS [37]

* OPLS All atoms for proteins [38] and OPLS All atoms for RNA [39]

Any of these data set can be used to populate on demand the force field to be designed using **atomes**, it is also possible to use any set of custom, user defined, parameters.

## 5. Case studies

This section regroups examples cases that can be reproduced using the example files available on **atomes** website: https://atomes.ipcms.fr/examples/
5.1. Getting information on selected structural features: g(r) in g-SiO₂

The following example illustrates how **atomes** can be use to retrieve information on selected structural
features:

1. Open the **atomes** project file for the system "gSiO₂ with ring statistics and custom color map, 3000 atoms"

<figure><img src="image_11.png" /></figure>

Note that the "Toolboxes" dialog is active and some results, from calculation performed previously
and stored in the project file, are available, including for the radial distribution function g(r).

2. Go back to the 3D window of the g-SiO₂ model, for clarity purpose change color map to standard chemical species: from the "OpenGL -> Color Scheme(s)" menu, or press `a` as many times as required. Then open the "Environments configuration" window: from the "Chemistry" menu or press `Ctrl` + `e`, and open the tab labelled "King's ring(s)[KR]".
<figure><img src="image_12.png" /></figure>

This tab provides interactors with King's ring statistics calculation results: color of the ring's polyhedra, and then options to show/hide, label/unlabel, or select/unselect atom(s) involved in any ring(s) of the corresponding size.

3. "Pick" all atoms in ring(s) of size 6: atoms in the 3D window are then selected and highlighted in light blue color.

<figure><img src="image_13.png" /></figure>

4. Go back to the 3D window, and mouse right click on any selected atom, then browse the contextual menu that pops up to "Edit as New Project", then select "All Selected Atom(s)/Bond(s)"
<figure><img src="image_14.png" /></figure>

<figure><img src="image_15.png" /></figure>

<figure><img src="image_16.png" /></figure>

This will create a new **atomes** project that will immediately be inserted in the program's workspace, and the corresponding 3D window will appear.

This new model contains all atoms involved in King's rings of size 6 selected previously in the disordered SiO₂ model.

5. From the main interface open the "Edit" menu and select "Box and Periodicity" to reproduce the periodicity of the initial model describing properly the simulation box (a = b = c = 35.6621 Å, α = β = γ = 90°, and be sure to use Periodic Boundary Conditions), then apply changes.

<figure><img src="image_17.png" /></figure>

The new model now uses periodic boundary conditions, if required the box can be displayed in the 3D window using the corresponding menu button: "Model -> Box -> Show/Hide".

6. Again from the main interface open the "Analyze" menu, then select "g(r) / G(r)", to open the
associated calculation dialog. Set parameter(s) to acceptable value(s) and run the analysis.

<figure><img src="image_18.png" /></figure>

7. When the calculation is completed, close the dialog, and note that the content of the "Toolboxes" dialog is updated, the results of the calculation being available:

<figure><img src="image_19.png" /></figure>

In the "Toolboxes" dialog open the result of the calculation to display the g(r) of the active project, in this case the new model created from the atom selection.
8. On the curve window press the mouse right click, browse the menu to "Add Data Set -> gSiO₂ -> g(r) neutrons" to add the corresponding data set to the representation:

<figure><img src="image_20.png" /></figure>

Note that projects opened in **atomes** share data. Therefore calculation results, from any model in the workspace and provided that the calculations have been performed, can be compared easily.

In this example it allows to compare the g(r) for the g-SiO₂ system with a partial contribution from the atoms involved in King's rings of size 6.

Comprehensive layout options are available and presentation can be clarified, each data set customized, so that the results of the analysis are quickly publication ready (for other examples see fig. 2).

## 5.2. Building a crystal, then creating and passivating a surface

1. Create a new empty project: "Workspace -> Project -> New" or press `Ctrl` + `n`, then open the crystal builder for the new, and empty, 3D window: "Tools -> Edit -> Crystal Builder"
<figure><img src="image_21.png" /></figure>

2. Adjust parameters to selected space group and corresponding settings, in this example large diamond-like crystal: Cubic, Face-centered, space group N°227 "Fd-3m (1)"

Select the object(s) to be inserted at crystalline position(s), in this example C atom(s), note that in **atomes** it is also possible to use molecular fragments inserted from the software library or from any project opened in the workspace (see Fig. 6). If needed adjust position, and / or occupancy, then remember to select the object(s) to be actually inserted when building the crystal by clicking on "Insert". Then simply click on "Build".

<figure><img src="image_22.png" /></figure>

The 3D window is populated with the newly created structure, in this example a "20×20×20" supercell of pure diamond.

3. To create a surface in this crystalline material, open the dedicated tool: "Tools -> Edit -> Cell -> Cut Slab"
<figure><img src="image_23.png" /></figure>

4. Adjust the shape of the slab to "Cylinder", in the "Size" options adjust the cylinder length and radius to 80 Å and 15 Å respectively. You can display the slab using the "Show/Hide slab" interactor, also export the results of the cutting/passivating in a new project by activating the corresponding option.

Check on "Passivate surface" and, in the option dialog that immediately opens, and as illustrated select to passivate empty C-C bonds created when cutting the slab with water molecule.

<figure><img src="image_24.png" /></figure>

Then just click on "Cut this slab now !" to create a new project, that will contain the new material: a C diamond cell where the atoms inside the cylinder are removed, creating a surface, and where non-bridging bonds have been passivated using H₂O molecules.
5. Newly inserted water molecules, under selection, appear in light blue. If you rotate to model box to face right, water molecules appear perfectly aligned. To create disorder open the "Random Move" tab of the "Model Edition" dialog: "Tools -> Edit -> Atoms -> Random Move"

<figure><img src="image_25.png" /></figure>

6. This interface allows to search for, and move randomly, atom(s) or group of atom(s), selection target(s) appearing in the table below. Also note that, quite conveniently, "All selected atoms" are by default targets of the action(s) to be performed.

To work on water molecules set the search parameters as follow:

* "For": use "Group of atoms: all" to work on group of atoms, and not atom(s) individually, and to display a single interactor for all object(s) instead of a list detailed list.

* "Filter": use "Partial coordination", to display a list of partial coordination(s) matching previously set criteria.

Then selected to "Rotate" all `"O[H₂]"` coordination spheres, that is all water molecules, set a maximum Mean Square Displacement by adjusting the corresponding parameter, and if required specify how many times the process is to be repeated.
<figure><img src="image_26.png" /></figure>

Then simply click on "Move atom(s)" to rotate randomly and separately each water molecule in the model.

## 6. Conclusion

**atomes** is a open source software that regroups a number of tools dedicated to the study of atomic scale models. From the creation of the model to the analysis of the system **atomes** can help the scientist toward designing new materials. It can also help to fine-tune molecular dynamics calculations with an advanced system of helpers to guide users in preparing classical, *ab-initio* or hybrid QM-MM (available soon) calculations.

Finally it is worth mentioning that **atomes** introduces for the first time several tools to the open source community such as the possibility to handle and analyze NPT trajectories, the crystal builder using molecular fragment(s) or the surface creation and passivation utility.

## 7. Distribution and documentation

**atomes** is an open source program licensed under the terms of the GNU Affero General Public Licence v3 [68], installation packages and source code are freely and easily accessible by the entire scientific community. The latest version to date 1.1.17.

Furthermore **atomes** is distributed by both Red Hat and Debian official software repositories, making it
extremely easy to installed on any Linux distribution via its official software management utility, or, using
the command line:

* Red Hat based Linux:

`user@localhost:~$ sudo dnf install atomes`

* Debian<fnref n="1" /> based Linux:

`user@localhost:~$ sudo apt install atomes`

Other **atomes** binaries are available for download from the official web site: http://atomes.ipcms.fr/

atomes sources are hosted on GitHub:

* Development version: https://github.com/Slookeur/atomes/

* Release version: https://github.com/Slookeur/atomes-GNU/

As are the comprehensive documentations:

* User manual: https://slookeur.github.io/atomes-doc.

* Code source documentation: https://slookeur.github.io/atomes-doxygen

<footnote n="1">¹For Linux distributions based on Debian 12 and below it might be required to activate the backports repository, see
https://atomes.ipcms.fr/download for details.</footnote>
References

[1] W. Humphrey, A. Dalke, and K. Schulten. *Journal of Molecular Graphics*, 14(1):33–38, 1996.

[2] A. Stukowski. *Modelling and simulation in materials science and engineering*, 18(1):015012, 2010.

[3] M. D. Hanwell, D. E. Curtis, D. C. Lonie, T. Vandermeersch, E. Zurek, and G. R. Hutchison. *Journal of Cheminformatics*, 4:17, 2012.

[4] https://jp-minerals.org/vesta/en/.

[5] Jmol: an open-source java viewer for chemical structures in 3d. http://www.jmol.org/.

[6] https://www.3ds.com/products/biovia/materials-studio.

[7] https://www.schrodinger.com/.

[8] https://www.samson-connect.net/.

[9] https://www.chemcomp.com/en/products.htm.

[10] https://www.scd.stfc.ac.uk/Pages/DL_POLY.aspx.

[11] https://lammps.sandia.gov/.

[12] http://www.cpmd.org.

[13] http://cp2k.berlios.de.

[14] W. D. Cornell, P. Cieplak, C. I. Bayly, I. R. Gould, K. M. Merz, D. M. Ferguson, D. C. Spellmeyer, T. Fox, J. W. Caldwell, and P. A. Kollman. *J. Am. Chem. Soc.*, 117(19):5179–5197, 1995. doi: 10.1021/ja00124a002.

[15] J. Wang, P. Cieplak, and P. A. Kollman. *J. Comp. Chem.*, 21(12):1049–1074. doi: https://doi.org/10.1002/1096-987X(200009)21:12<1049::AID-JCC3>3.0.CO;2-F.

[16] A. D. MacKerell, D. Bashford, M. Bellott, R. L. Dunbrack, J. D. Evanseck, M. J. Field, S. Fischer, J. Gao, H. Guo, S. Ha, D. Joseph-McCarthy, L. Kuchnir, K. Kuczera, F. T. K. Lau, C. Mattos,
S. Michnick, T. Ngo, D. T. Nguyen, B. Prodhom, W. E. Reiher, B. Roux, M. Schlenkrich, J. C. Smith, R. Stote, J. Straub, M. Watanabe, J. Wiórkiewicz-Kuczera, D. Yin, and M. Karplus. *J. Phys. Chem. B*, 102(18):3586–3616, 1998. doi: 10.1021/jp973084f.

[17] A. D. Mackerell, M. Feig, and C. L. Brooks III. *J. Comp. Chem.*, 25(11):1400–1415. doi: https://doi.org/10.1002/jcc.20065.

[18] O. Guvench, S. S. Mallajosyula, E. P. Raman, E. Hatcher, K. Vanommeslaeghe, T. J. Foster, F. W. Jamison, and A. D. MacKerell. *J. Chem. Theo. Comp.*, 7(10):3162–3180, 2011. doi: 10.1021/ct200328p.

[19] S. S. Mallajosyula, O. Guvench, E. Hatcher, and A. D. MacKerell. *J. Chem. Theo. Comp.*, 8(2):759–776, 2012. doi: 10.1021/ct200792v.

[20] E. P. Raman, O. Guvench, and A. D. MacKerell. *J. Phys. Chem. B*, 114(40):12981–12994, 2010. doi: 10.1021/jp105758h.

[21] O. Guvench, E. Hatcher, R. M. Venable, R. W. Pastor, and A. D. MacKerell. *J. Chem. Theo. Comp.*, 5(9):2353–2370, 2009. doi: 10.1021/ct900242e.

[22] K. Vanommeslaeghe, E. Hatcher, C. Acharya, S. Kundu, S. Zhong, J. Shim, E. Darian, O. Guvench, P. Lopes, I. Vorobyov, and A. D. Mackerell Jr. *J. Comp. Chem.*, 31(4):671–690. doi: https://doi.org/10.1002/jcc.21367.

[23] K. Vanommeslaeghe and A. D. MacKerell. *J. Chem. Inf. Mod.*, 52(12):3144–3154, 2012. doi: 10.1021/ci300363c.

[24] K. Vanommeslaeghe, E. Prabhu Raman, and A. D. MacKerell. *J. Chem. Inf. Mod.*, 52(12):3155–3168, 2012. doi: 10.1021/ci3003649.

[25] W. Yu, X. He, K. Vanommeslaeghe, and A. D. MacKerell. *J. Comp. Chem.*, 33(31):2451–2468. doi: https://doi.org/10.1002/jcc.23067.
[26] I. Soteras Gutiérrez, Lin F. Y., K. Vanommeslaeghe, J. A. Lemkul, Armacost K. A., Brooks C. L., and A. D. MacKerell. *Bioorg. Med. Chem.*, 24(20):4812–4825, 2016. doi: https://doi.org/10.1016/j.bmc.2016.06.034.

[27] J. B. Klauda, R. M. Venable, J. A. Freites, J. W. O’Connor, D. J. Tobias, C. Mondragon-Ramirez, I. Vorobyov, A. D. MacKerell, and R. W. Pastor. *J. Phys. Chem. B*, 114(23):7830–7843, 2010. doi: 10.1021/jp101759q.

[28] K. Hart, N. Foloppe, C. M. Baker, E. J. Denning, L. Nilsson, and A. D. MacKerell. *J. Chem. Theo. Comp.*, 8(1):348–362, 2012. doi: 10.1021/ct200723y.

[29] E. J. Denning, U. D. Priyakumar, L. Nilsson, and A. D. Mackerell. *J. Comp. Chem.*, 32(9):1929–1943. doi: https://doi.org/10.1002/jcc.21777.

[30] R. B. Best, X. Zhu, J. Shim, P. E. M. Lopes, J. Mittal, M. Feig, and A. D. MacKerell. *J. Chem. Theo. Comp.*, 8(9):3257–3273, 2012. doi: 10.1021/ct300400x.

[31] J. Huang, S. Rauscher, G. Nawrocki, T. Ran, M. Feig, B. L. de Groot, H. Grubmüller, and A. D. MacKerell. *Nat. Methods*, 14:71–73, 2017. doi: 10.1038/nmeth.406.

[32] P. E. M. Lopes, V. Murashov, M. Tazi, E. Demchuk, and A. D. MacKerell. *J. Phys. Chem. B*, 110(6): 2782–2792, 2006. doi: 10.1021/jp055341j.

[33] A. T. Hagler, S. Lifson, and P. Dauber. *J. Am. Chem. Soc.*, 101(18):5122–5130, 1979. doi: 10.1021/ja00512a002.

[34] P. Dauber-Osguthorpe, V. A. Roberts, D. J. Osguthorpe, J. Wolff, M. Genest, and A. T. Hagler. *Proteins: Structure, Function, and Bioinformatics*, 4(1):31–47. doi: https://doi.org/10.1002/prot.340040106.

[35] J. R. Maple, U. Dinur, and A. T. Hagler. *Proc. Nat. Ac. Sci.*, 85(15):5350–5354, 1988. doi: 10.1073/pnas.85.15.5350.

[36] H. Sun, S. J. Mumby, J. R. Maple, and A. T. Hagler. *J. Am. Chem. Soc.*, 116(7):2978–2987, 1994. doi: 10.1021/ja00086a030.
[37] H. Sun. *J. Phys. Chem. B*, 102(38):7338-7364, 1998. doi: 10.1021/jp980939v.

[38] M. J. Robertson, J. Tirado-Rives, and W. L. Jorgensen. *J. Chem. Theo. Comp.*, 11(7):3499-3509, 2015. doi: 10.1021/acs.jctc.5b00356.

[39] M. J. Robertson, Y. Qian, M. C. Robinson, J. Tirado-Rives, and W. L. Jorgensen. *J. Chem. Theo. Comp.*, 15(4):2734-2742, 2019. doi: 10.1021/acs.jctc.9b00054.

[40] http://www.gtk.org/.

[41] https://www.openmp.org/.

[42] https://www opengl.org/.

[43] https:// Committee on Financial Regulation and Supervision of the European Union (FIRSU).

[44] Minnesota Supercomputer Center, 1993.

[45] CambridgeSoft. *Chem3D*, pages Cambridge Scientific Computing, Cambridge Massachusetts, USA, 2009.

[46] http://cms.mpi.univie.ac.at/vasp/.

[47] S. Le Roux and V. Petkov. *J. Appl. Cryst.*, 43:181-185, 2010.

[48] M. P. Allen and D. J. Tildesley. *Computer simulation of liquids*. Oxford science publications, 1987.

[49] P. S. Salmon. *J. Non-Cryst. Solids.*, 353:2959-2974, 2007.

[50] M. T. Dove, M. G. Tucker, and D. A. Keen. *Eur. J. Mat.*, 14:331-348, 2002.

[51] B. Thijsse. *J. Appl. Cryst.*, 17:61-76, 1984.

[52] T. E. Faber and Ziman J. M. *Phil. Mag.*, 11(109):153-173, 1965.

[53] N. W. Ashcroft and D. C. Langreth. *Phys. Rev.*, 156(3):685-692, 1967.

[54] N. W. Ashcroft and D. C. Langreth. *Phys. Rev.*, 159(3):500-510, 1967.

[55] N. W. Ashcroft and D. C. Langreth. *Phys. Rev.*, 166(3):934, 1968.
[56] A. B. Bhatia and D. E. Thornton. *Phys. Rev. B*, 2(8):3004–3012, 1970.

[57] S. V. King. *Nature*, 213:1112, 1967.

[58] D. S. Franzblau. *Phys. Rev. B*, 44(10):4925–4930, 1991.

[59] L. Guttman. *J. Non-Cryst. Solids.*, 116:145–147, 1990.

[60] K. Goetzke and H. J. Klein. *J. Non-Cryst. Solids.*, 127:215–220, 1991.

[61] X. Yuan and A. N. Cormack. *Comp. Mat. Sci.*, 24:343–360, 2002.

[62] F. Wooten. *Acta Cryst.* A, 58(4):346–351, 2002.

[63] S. Le Roux and P. Jund. *Comp. Mat. Sci.*, 49:70–83, 2010.

[64] P. Steinhardt, D. R. Nelson, and M. Ronchetti. *Phys. Rev. B*, 28(2):784–805, 1983.

[65] F. H. M. van Roon, C. Massobrio, E. de Wolff, and S. W. de Leeuw. *J. Chem. Phys.*, 113(13):5425, 2000.

[66] S. Le Roux, A. Bouzid, M. Boero, and C. Massobrio. *J. Chem. Phys.*, 138(17):174505, 2013.

[67] S. Le Roux, A. Zeidler, P. S. Salmon, M. Boero, M. Micoulaut, and C. Massobrio. *Phys. Rev. B*, 84: 134203, 2011. doi: 10.1103/PhysRevB.84.134203.

[68] Free Software Foundation, Inc. GNU General Public Licence v3, page http://www.gnu.org/licensesSTALL.html, 2007.