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list possible pair styles with SPC Howto. Add comment about cutof vs. long-range coulomb

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Axel Kohlmeyer
2025-06-20 04:24:13 -04:00
parent 97d7e9e4a1
commit 18455d07fe
4 changed files with 33 additions and 6 deletions
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16
doc/src/Howto_spc.rst
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@ -8,6 +8,18 @@ the two O-H bonds and the H-O-H angle rigid. A bond style of
*harmonic* and an angle style of *harmonic* or *charmm* should also be *harmonic* and an angle style of *harmonic* or *charmm* should also be
used. used.
One suitable pair style with cutoff Coulomb would for instance be:
* :doc:`pair_style lj/cut/coul/cut <pair_lj_cut_coul>`
These commands are examples for a long-range Coulomb model:
* :doc:`pair_style lj/cut/coul/long <pair_lj_cut_coul>`
* :doc:`pair_style lj/cut/coul/long/soft <pair_fep_soft>`
* :doc:`kspace_style pppm <kspace_style>`
* :doc:`pair_style lj/long/coul/long <pair_lj_long>`
* :doc:`kspace_style pppm/disp <kspace_style>`
These are the additional parameters (in real units) to set for O and H These are the additional parameters (in real units) to set for O and H
atoms and the water molecule to run a rigid SPC model. atoms and the water molecule to run a rigid SPC model.
@ -39,7 +51,9 @@ the SPC and SPC/E models.
Below is the code for a LAMMPS input file and a molecule file Below is the code for a LAMMPS input file and a molecule file
(``spce.mol``) of SPC/E water for use with the :doc:`molecule command (``spce.mol``) of SPC/E water for use with the :doc:`molecule command
<molecule>` demonstrating how to set up a small bulk water system for <molecule>` demonstrating how to set up a small bulk water system for
SPC/E with rigid bonds. SPC/E with rigid bonds. For simplicity and speed the example uses a
cutoff Coulomb. Most production simulations require long-range Coulomb
instead.
.. code-block:: LAMMPS .. code-block:: LAMMPS

15
doc/src/Howto_tip3p.rst
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@ -5,17 +5,24 @@ The TIP3P water model as implemented in CHARMM :ref:`(MacKerell)
<howto-tip3p>` specifies a 3-site rigid water molecule with charges and <howto-tip3p>` specifies a 3-site rigid water molecule with charges and
Lennard-Jones parameters assigned to each of the three atoms. Lennard-Jones parameters assigned to each of the three atoms.
A suitable pair style with cutoff Coulomb would be: One suitable pair style with cutoff Coulomb would for instance be:
* :doc:`pair_style lj/cut/coul/cut <pair_lj_cut_coul>` * :doc:`pair_style lj/cut/coul/cut <pair_lj_cut_coul>`
or these commands for a long-range Coulomb model: These commands are examples for a long-range Coulomb model:
* :doc:`pair_style lj/cut/coul/long <pair_lj_cut_coul>` * :doc:`pair_style lj/cut/coul/long <pair_lj_cut_coul>`
* :doc:`pair_style lj/cut/coul/long/soft <pair_fep_soft>` * :doc:`pair_style lj/cut/coul/long/soft <pair_fep_soft>`
* :doc:`kspace_style pppm <kspace_style>` * :doc:`kspace_style pppm <kspace_style>`
* :doc:`pair_style lj/long/coul/long <pair_lj_long>`
* :doc:`kspace_style pppm/disp <kspace_style>` * :doc:`kspace_style pppm/disp <kspace_style>`
And these pair styles are compatible with the CHARMM force field:
* :doc:`pair_style lj/charmm/coul/charmm <pair_charmm>`
* :doc:`pair_style lj/charmm/coul/long <pair_charmm>`
* :doc:`pair_style lj/charmmfsw/coul/long <pair_charmm>`
In LAMMPS the :doc:`fix shake or fix rattle <fix_shake>` command can be In LAMMPS the :doc:`fix shake or fix rattle <fix_shake>` command can be
used to hold the two O-H bonds and the H-O-H angle rigid. A bond style used to hold the two O-H bonds and the H-O-H angle rigid. A bond style
of :doc:`harmonic <bond_harmonic>` and an angle style of :doc:`harmonic of :doc:`harmonic <bond_harmonic>` and an angle style of :doc:`harmonic
@ -100,7 +107,9 @@ ignored.
Below is the code for a LAMMPS input file and a molecule file Below is the code for a LAMMPS input file and a molecule file
(``tip3p.mol``) of TIP3P water for use with the :doc:`molecule command (``tip3p.mol``) of TIP3P water for use with the :doc:`molecule command
<molecule>` demonstrating how to set up a small bulk water system for <molecule>` demonstrating how to set up a small bulk water system for
TIP3P with rigid bonds. TIP3P with rigid bonds. For simplicity and speed the example uses a
cutoff Coulomb. Most production simulations require long-range Coulomb
instead.
.. code-block:: LAMMPS .. code-block:: LAMMPS

4
doc/src/Howto_tip4p.rst
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@ -167,7 +167,9 @@ cutoffs are set in the :doc:`pair_style lj/cut/tip4p/long
Below is the code for a LAMMPS input file using the implicit method and Below is the code for a LAMMPS input file using the implicit method and
the :ref:`TIP3P molecule file <tip3p_molecule>`. Because the TIP4P the :ref:`TIP3P molecule file <tip3p_molecule>`. Because the TIP4P
charges are different from TIP3P they need to be reset (or the molecule charges are different from TIP3P they need to be reset (or the molecule
file changed): file changed). For simplicity and speed the example uses a cutoff
Coulomb. Most production simulations require long-range Coulomb
instead.
.. code-block:: LAMMPS .. code-block:: LAMMPS

4
doc/src/Howto_tip5p.rst
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@ -87,7 +87,9 @@ atom style full or use :doc:`fix property/atom mol <fix_property_atom>`
so that fix rigid/small can identify rigid bodies by their molecule ID. so that fix rigid/small can identify rigid bodies by their molecule ID.
Also a :doc:`neigh_modify exclude <neigh_modify>` command is added to Also a :doc:`neigh_modify exclude <neigh_modify>` command is added to
exclude computing intramolecular non-bonded interactions, since those exclude computing intramolecular non-bonded interactions, since those
are removed by the rigid fix anyway: are removed by the rigid fix anyway. For simplicity and speed the
example uses a cutoff Coulomb. Most production simulations require
long-range Coulomb instead.
.. code-block:: LAMMPS .. code-block:: LAMMPS