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Add example for water orientation (#170)
* Add example for water orientatio * Update examples/water-pulsed/data/grompp.mdp * Some proofread
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‎docs/src/software/gromacs.sec‎

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GROMACS
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=======
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GROMACS is a versatile and highly optimized molecular dynamics (MD) engine designed for
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classical simulations. It is widely recognized for its exceptional performance,
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scalability, and efficiency, making it suitable for use on systems ranging from laptops
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to high-performance computing (HPC) clusters. Originally developed for biomolecular
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simulations, GROMACS is commonly used in fields such as biochemistry, biophysics, and
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structural biology to study proteins, lipids, and nucleic acids.
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In addition to its focus on biomolecular systems, GROMACS supports a wide range of force
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fields and can simulate non-biological systems such as polymers and materials. It
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includes tools for preprocessing, trajectory analysis, and visualization, providing a
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comprehensive suite for MD workflows. Its open-source nature and active community ensure
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continuous development and support.
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- examples/water-pulsed/water-pulsed

‎docs/src/software/index.rst‎

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Recipes grouped by software used
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================================
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Cookbook recipes often combine multiple modeling tools.
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Here you can find them organized based on the software
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they use. They may give you ideas on how to use them
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in your own atomistic cooking.
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.. toctree::
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:maxdepth: 1
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:hidden:
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i-pi
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chemiscope
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featomic
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scikit-matter
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cp2k
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lammps
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metatensor
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plumed
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torch-pme
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:doc:`i-pi`
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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.. card-carousel:: 3
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.. card:: Atomistic Water Model for Molecular Dynamics
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:link: ../examples/water-model/water-model
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:link-type: doc
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:text-align: center
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:shadow: md
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.. image:: ../examples/water-model/images/thumb/sphx_glr_water-model_thumb.png
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:alt: In this example, we demonstrate how to construct a metatensor atomistic model for flexible three and four-point water model, with parameters optimized for use together with quantum-nuclear-effects-aware path integral simulations (cf. Habershon et al., JCP (2009)). The model also demonstrates the use of torch-pme, a Torch library for long-range interactions, and uses the resulting model to perform demonstrative molecular dynamics simulations.
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:class: gallery-img
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:doc:`chemiscope`
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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.. card-carousel:: 3
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.. card:: Atomistic Water Model for Molecular Dynamics
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:link: ../examples/water-model/water-model
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:link-type: doc
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:text-align: center
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:shadow: md
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.. image:: ../examples/water-model/images/thumb/sphx_glr_water-model_thumb.png
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:alt: In this example, we demonstrate how to construct a metatensor atomistic model for flexible three and four-point water model, with parameters optimized for use together with quantum-nuclear-effects-aware path integral simulations (cf. Habershon et al., JCP (2009)). The model also demonstrates the use of torch-pme, a Torch library for long-range interactions, and uses the resulting model to perform demonstrative molecular dynamics simulations.
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:class: gallery-img
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:doc:`featomic`
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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.. card-carousel:: 3
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:doc:`scikit-matter`
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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.. card-carousel:: 3
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:doc:`cp2k`
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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.. card-carousel:: 3
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:doc:`lammps`
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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.. card-carousel:: 3
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.. card:: Atomistic Water Model for Molecular Dynamics
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:link: ../examples/water-model/water-model
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:link-type: doc
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:text-align: center
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:shadow: md
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.. image:: ../examples/water-model/images/thumb/sphx_glr_water-model_thumb.png
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:alt: In this example, we demonstrate how to construct a metatensor atomistic model for flexible three and four-point water model, with parameters optimized for use together with quantum-nuclear-effects-aware path integral simulations (cf. Habershon et al., JCP (2009)). The model also demonstrates the use of torch-pme, a Torch library for long-range interactions, and uses the resulting model to perform demonstrative molecular dynamics simulations.
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:class: gallery-img
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:doc:`metatensor`
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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.. card-carousel:: 3
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.. card:: Atomistic Water Model for Molecular Dynamics
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:link: ../examples/water-model/water-model
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:link-type: doc
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:text-align: center
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:shadow: md
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.. image:: ../examples/water-model/images/thumb/sphx_glr_water-model_thumb.png
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:alt: In this example, we demonstrate how to construct a metatensor atomistic model for flexible three and four-point water model, with parameters optimized for use together with quantum-nuclear-effects-aware path integral simulations (cf. Habershon et al., JCP (2009)). The model also demonstrates the use of torch-pme, a Torch library for long-range interactions, and uses the resulting model to perform demonstrative molecular dynamics simulations.
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:class: gallery-img
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:doc:`plumed`
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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.. card-carousel:: 3
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:doc:`torch-pme`
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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.. card-carousel:: 3
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.. card:: Atomistic Water Model for Molecular Dynamics
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:link: ../examples/water-model/water-model
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:link-type: doc
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:text-align: center
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:shadow: md
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.. image:: ../examples/water-model/images/thumb/sphx_glr_water-model_thumb.png
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:alt: In this example, we demonstrate how to construct a metatensor atomistic model for flexible three and four-point water model, with parameters optimized for use together with quantum-nuclear-effects-aware path integral simulations (cf. Habershon et al., JCP (2009)). The model also demonstrates the use of torch-pme, a Torch library for long-range interactions, and uses the resulting model to perform demonstrative molecular dynamics simulations.
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:class: gallery-img
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‎docs/src/topics/analysis.sec‎

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- examples/lpr/lpr
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- examples/roy-gch/roy-gch
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- examples/rotate-equivariants/rotate-equivariants
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- examples/water-pulsed/water-pulsed

‎docs/src/topics/index.rst‎

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Recipes grouped by topic
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========================
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You can navigate through the various recipes grouped
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in thematic areas, including classes of simulation problems
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and of modeling techniques. Recipes may be listed in
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more than one area, when relevant.
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.. toctree::
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:maxdepth: 1
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:hidden:
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sampling
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analysis
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ml-models
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universal
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nqes
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:doc:`sampling`
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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.. card-carousel:: 3
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.. card:: Atomistic Water Model for Molecular Dynamics
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:link: ../examples/water-model/water-model
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:link-type: doc
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:text-align: center
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:shadow: md
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.. image:: ../examples/water-model/images/thumb/sphx_glr_water-model_thumb.png
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:alt: In this example, we demonstrate how to construct a metatensor atomistic model for flexible three and four-point water model, with parameters optimized for use together with quantum-nuclear-effects-aware path integral simulations (cf. Habershon et al., JCP (2009)). The model also demonstrates the use of torch-pme, a Torch library for long-range interactions, and uses the resulting model to perform demonstrative molecular dynamics simulations.
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:class: gallery-img
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:doc:`analysis`
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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.. card-carousel:: 3
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.. card:: Water orientation in a pulsed electric field
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:link: ../examples/water-pulsed/water-pulsed
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:link-type: doc
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:text-align: center
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:shadow: md
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.. image:: ../examples/water-pulsed/images/thumb/sphx_glr_water-pulsed_thumb.png
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:alt: Energy dissipation in water is very fast and more efficient than in many other liquids. This behavior is commonly attributed to the intermolecular interactions associated with hydrogen bonding. This effect has been studied intensively by experiments, ab initio, and classical simulations in the work by Elgabarty et al.. Here, we will re run some of the classical force field molecular dynamics (MD) simulations of the paper using the GROMACS package to compute the timeseries of the dipole moments as well as the energy.
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:class: gallery-img
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:doc:`ml-models`
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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.. card-carousel:: 3
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:doc:`universal`
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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.. card-carousel:: 3
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:doc:`nqes`
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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.. card-carousel:: 3
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‎examples/water-pulsed/.gitignore‎

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# GROMACS files
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*.cpt
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*.edr
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*.gro
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*.log
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*.mdp
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*.top
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*.tpr
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*.trr
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*.xtc
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\#*
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!data/grompp.mdp
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# MDAnalysis offset files
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*.lock
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*.npz

‎examples/water-pulsed/README.rst‎

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Water orientation in a pulsed electric field
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============================================
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Simulate water reorientation and energy dissipation in a pulsed electric field.

‎examples/water-pulsed/data/conf.gro.gz‎

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‎examples/water-pulsed/data/grompp.mdp‎

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; Integrator
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; ===================================================================
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integrator = md
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; MD Running Parameters
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; ===================================================================
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dt = 0.002
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nsteps = 5000
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comm-mode = linear ; Remove center of mass translation
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nstcomm = 500 ; Do not remove center of mass during pulse
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; Output control
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; frequency for coords (x), velocities (v) and forces (f)
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; ===================================================================
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nstxout-compressed = 50
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nstlog = 1000
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nstenergy = 50
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nstcalcenergy = 50
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; Neighbor searching
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; ===================================================================
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cutoff-scheme = Verlet
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rlist = 0.9
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; Electrostatics
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; ===================================================================
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coulombtype = pme
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rcoulomb = 0.9
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; VdW
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; ===================================================================
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vdw-type = Cut-off
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rvdw = 0.9
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vdw-modifier = Potential-shift-Verlet
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; Constraints
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; ===================================================================
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constraints = h-bonds
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constraint-algorithm = LINCS
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;Electric fields
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; ===================================================================
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electric-field-x = 0.5 1.0 5.0 0.5 ; E0 omega t0 sigma

‎examples/water-pulsed/environment.yml‎

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channels:
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- conda-forge
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dependencies:
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- python=3.12
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- gromacs
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- pip
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- pip:
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- maicos
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- pyedr

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