diff --git a/doc/src/Howto_spc.rst b/doc/src/Howto_spc.rst index f84d7797d2..eb44e41de0 100644 --- a/doc/src/Howto_spc.rst +++ b/doc/src/Howto_spc.rst @@ -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 used. +One suitable pair style with cutoff Coulomb would for instance be: + +* :doc:`pair_style lj/cut/coul/cut ` + +These commands are examples for a long-range Coulomb model: + +* :doc:`pair_style lj/cut/coul/long ` +* :doc:`pair_style lj/cut/coul/long/soft ` +* :doc:`kspace_style pppm ` +* :doc:`pair_style lj/long/coul/long ` +* :doc:`kspace_style pppm/disp ` + 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. @@ -39,7 +51,9 @@ the SPC and SPC/E models. 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 ` 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 diff --git a/doc/src/Howto_tip3p.rst b/doc/src/Howto_tip3p.rst index 4b0346ea1a..a432146713 100644 --- a/doc/src/Howto_tip3p.rst +++ b/doc/src/Howto_tip3p.rst @@ -5,17 +5,24 @@ The TIP3P water model as implemented in CHARMM :ref:`(MacKerell) ` specifies a 3-site rigid water molecule with charges and 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 ` -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 ` * :doc:`pair_style lj/cut/coul/long/soft ` * :doc:`kspace_style pppm ` +* :doc:`pair_style lj/long/coul/long ` * :doc:`kspace_style pppm/disp ` +And these pair styles are compatible with the CHARMM force field: + +* :doc:`pair_style lj/charmm/coul/charmm ` +* :doc:`pair_style lj/charmm/coul/long ` +* :doc:`pair_style lj/charmmfsw/coul/long ` + In LAMMPS the :doc:`fix shake or fix rattle ` command can be used to hold the two O-H bonds and the H-O-H angle rigid. A bond style of :doc:`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 (``tip3p.mol``) of TIP3P water for use with the :doc:`molecule command ` 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 diff --git a/doc/src/Howto_tip4p.rst b/doc/src/Howto_tip4p.rst index 76c470d615..71f6605fb8 100644 --- a/doc/src/Howto_tip4p.rst +++ b/doc/src/Howto_tip4p.rst @@ -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 the :ref:`TIP3P molecule file `. Because the TIP4P 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 diff --git a/doc/src/Howto_tip5p.rst b/doc/src/Howto_tip5p.rst index 438e8b4088..9956b6fa0c 100644 --- a/doc/src/Howto_tip5p.rst +++ b/doc/src/Howto_tip5p.rst @@ -87,7 +87,9 @@ atom style full or use :doc:`fix property/atom mol ` so that fix rigid/small can identify rigid bodies by their molecule ID. Also a :doc:`neigh_modify exclude ` command is added to 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