162 lines
4.4 KiB
ReStructuredText
162 lines
4.4 KiB
ReStructuredText
TIP5P water model
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=================
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The five-point TIP5P rigid water model extends the :doc:`three-point
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TIP3P model <Howto_tip3p>` by adding two additional sites L, usually
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massless, where the charge associated with the oxygen atom is placed.
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These sites L are located at a fixed distance away from the oxygen atom,
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forming a tetrahedral angle that is rotated by 90 degrees from the HOH
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plane. Those sites thus somewhat approximate lone pairs of the oxygen
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and consequently improve the water structure to become even more
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"tetrahedral" in comparison to the :doc:`four-point TIP4P model
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<Howto_tip4p>`.
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A suitable pair style with cutoff Coulomb would be:
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* :doc:`pair_style lj/cut/coul/cut <pair_lj_cut_coul>`
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or these commands for a long-range model:
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* :doc:`pair_style lj/cut/coul/long <pair_lj_cut_coul>`
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* :doc:`pair_style lj/cut/coul/long/soft <pair_fep_soft>`
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* :doc:`kspace_style pppm <kspace_style>`
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* :doc:`kspace_style pppm/disp <kspace_style>`
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A TIP5P model *must* be run using a :doc:`rigid fix <fix_rigid>` since
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there is no other option to keep this kind of structure rigid in LAMMPS.
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In order to avoid that LAMMPS produces an error due to the massless L
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sites, those need to be assigned a tiny non-zero mass.
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The table below lists the force field parameters (in real :doc:`units
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<units>`) to for a the TIP5P model with a cutoff :ref:`(Mahoney)
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<Mahoney>` and the TIP5P-E model :ref:`(Rick) <Rick>` for use with a
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long-range Coulombic solver (e.g. Ewald or PPPM in LAMMPS).
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.. list-table::
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:header-rows: 1
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:widths: auto
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* - Parameter
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- TIP5P
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- TIP5P-E
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* - O mass (amu)
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- 15.9994
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- 15.9994
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* - H mass (amu)
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- 1.008
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- 1.008
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* - O charge (:math:`e`)
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- 0.0
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- 0.0
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* - L charge (:math:`e`)
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- -0.241
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- -0.241
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* - H charge (:math:`e`)
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- 0.241
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- 0.241
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* - LJ :math:`\epsilon` of OO (kcal/mole)
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- 0.1600
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- 0.1780
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* - LJ :math:`\sigma` of OO (:math:`\AA`)
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- 3.1200
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- 3.0970
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* - LJ :math:`\epsilon` of HH, LL, OH, OL, HL (kcal/mole)
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- 0.0
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- 0.0
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* - LJ :math:`\sigma` of HH, LL, OH, OL, HL (:math:`\AA`)
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- 1.0
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- 1.0
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* - :math:`r_0` of OH bond (:math:`\AA`)
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- 0.9572
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- 0.9572
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* - :math:`\theta_0` of HOH angle
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- 104.52\ :math:`^{\circ}`
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- 104.52\ :math:`^{\circ}`
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* - OL distance (:math:`\AA`)
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- 0.70
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- 0.70
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* - :math:`\theta_0` of LOL angle
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- 109.47\ :math:`^{\circ}`
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- 109.47\ :math:`^{\circ}`
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Below is the code for a LAMMPS input file for setting up a simulation of
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TIP5P water with a molecule file. Because of using :doc:`fix
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rigid/nvt/small <fix_rigid>` no bonds need to be defined and thus no
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extra storage needs to be reserved for them, but we need to switch to
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atom style full or use :doc:`fix property/atom mol <fix_property_atom>`
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so that fix rigid/nvt/small can identify rigid bodies by their molecule
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ID:
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.. code-block:: LAMMPS
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units real
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atom_style charge
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region box block -5 5 -5 5 -5 5
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create_box 3 box
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mass 1 15.9994
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mass 2 1.008
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mass 3 1.0e-100
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pair_style lj/cut/coul/cut 8.0
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pair_coeff 1 1 0.160 3.12
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pair_coeff 2 2 0.0 1.0
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pair_coeff 3 3 0.0 1.0
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fix mol all property/atom mol
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molecule water tip5p.mol
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create_atoms 0 random 33 34564 NULL mol water 25367 overlap 1.33
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timestep 0.20
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fix integrate all rigid/nvt/small molecule temp 300.0 300.0 1.0
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reset_timestep 0
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velocity all create 300.0 5463576
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thermo_style custom step temp press etotal density pe ke
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thermo 1000
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run 20000
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write_data tip5p.data nocoeff
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.. _tip5p_molecule:
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.. code-block::
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# Water molecule. Explicit TIP5P geometry for use with fix rigid
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5 atoms
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Coords
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1 0.00000 -0.06556 0.00000
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2 0.75695 0.52032 0.00000
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3 -0.75695 0.52032 0.00000
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4 0.00000 -0.46971 0.57154
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5 0.00000 -0.46971 -0.57154
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Types
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1 1 # O
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2 2 # H
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3 2 # H
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4 3 # L
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5 3 # L
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Charges
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1 0.000
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2 0.241
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3 0.241
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4 -0.241
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5 -0.241
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Wikipedia also has a nice article on `water models <https://en.wikipedia.org/wiki/Water_model>`_.
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----------
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.. _Mahoney:
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**(Mahoney)** Mahoney, Jorgensen, J Chem Phys 112, 8910 (2000)
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.. _Rick:
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**(Rick)** Rick, J Chem Phys 120, 6085 (2004)
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