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.. admonition:: Struggling with your molecular simulations project?
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:class: patreon
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Get guidance for your LAMMPS simulations and receive
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personalized |advice| for your project.
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.. |advice| raw:: html
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<a href="https://www.patreon.com/molecularsimulations" target="_blank">advice</a>

docs/sphinx/source/tutorial1/tutorial.rst

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constraint helps avoid close contacts between atoms, which can lead
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to excessively large forces and simulation instability.
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.. include:: ../shared/needhelp.rst
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Settings
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--------
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docs/sphinx/source/tutorial2/tutorial.rst

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atoms closer than this distance interact through the Lennard-Jones
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potential.
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The ``bond_style``, ``angle_style``, ``dihedral_style``, and ``improper_style``
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commands specify the different potentials used to constrain the relative
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positions of the atoms. The ``special_bonds`` command sets the weighting factors

docs/sphinx/source/tutorial3/tutorial.rst

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:ref:`carbon-nanotube-label`, sets the LJ and Coulomb
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weighting factors for the interaction between neighboring atoms.
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.. include:: ../shared/needhelp.rst
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Let us create a 3D simulation box of dimensions :math:`6 \times 3 \times 3 \; \text{nm}^3`,
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and make space for 8 atom types (2 for the water, 6 for the polymer), 7 bond types
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(1 for the water, 6 for the polymer), 8 angle types (1 for the water, 7 for the polymer),

docs/sphinx/source/tutorial4/tutorial.rst

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potential. Here, ``lj/cut/tip4p/long`` imposes a Lennard-Jones potential with
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a cut-off at :math:`12\,\text{Å}` and a long-range Coulomb potential.
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So far, the commands are relatively similar to those in the previous tutorial,
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:ref:`all-atoms-label`, with two major differences: the use
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of ``lj/cut/tip4p/long`` instead of ``lj/cut/coul/long``, and ``pppm/tip4p``

docs/sphinx/source/tutorial5/tutorial.rst

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Some basic parameters are defined (``units`` and ``atom_style``),
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and a **.data** file is imported by the ``read_data`` command.
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The initial topology given by |silica_data_5|
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is a small amorphous silica structure. This structure was created using a force field called
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Vashishta :cite:`vashishta1990interaction`. If you open the **silica.data**

docs/sphinx/source/tutorial6/tutorial.rst

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pair style. The Vashishta potential implicitly models atomic bonds through
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energy terms dependent on interatomic distances and angles :cite:`vashishta1990interaction`.
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.. include:: ../shared/needhelp.rst
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Let us create a box for two atom types, ``Si``
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of mass 28.0855 g/mol and ``O`` of mass 15.9994 g/mol.
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Add the following lines to **generate.lmp**:

docs/sphinx/source/tutorial7/tutorial.rst

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position-dependent repulsive force that makes the center of the box a less
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favorable area to explore.
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Basic LAMMPS parameters
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-----------------------
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