153 lines
3.3 KiB
ReStructuredText
153 lines
3.3 KiB
ReStructuredText
SPC and SPC/E water model
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=========================
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The SPC water model specifies a 3-site rigid water molecule with
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charges and Lennard-Jones parameters assigned to each of the three atoms.
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In LAMMPS the :doc:`fix shake <fix_shake>` command can be used to hold
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the two O-H bonds and the H-O-H angle rigid. A bond style of
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*harmonic* and an angle style of *harmonic* or *charmm* should also be
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used.
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These are the additional parameters (in real units) to set for O and H
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atoms and the water molecule to run a rigid SPC model.
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| O mass = 15.9994
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| H mass = 1.008
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| O charge = -0.820
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| H charge = 0.410
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| LJ :math:`\epsilon` of OO = 0.1553
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| LJ :math:`\sigma` of OO = 3.166
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| LJ :math:`\epsilon`, :math:`\sigma` of OH, HH = 0.0
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| :math:`r_0` of OH bond = 1.0
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| :math:`\theta_0` of HOH angle = 109.47\ :math:`^{\circ}`
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Note that as originally proposed, the SPC model was run with a 9
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Angstrom cutoff for both LJ and Coulomb terms. It can also be used
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with long-range electrostatic solvers (e.g. Ewald or PPPM in LAMMPS)
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without changing any of the parameters above, although it becomes
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a different model in that mode of usage.
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The SPC/E (extended) water model is the same, except
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the partial charge assignments change:
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| O charge = -0.8476
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| H charge = 0.4238
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See the :ref:`(Berendsen2) <howto-Berendsen>` reference for more details on both
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the SPC and SPC/E models.
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Below is the code for a LAMMPS input file and a molecule file
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(``spce.mol``) of SPC/E water for use with the :doc:`molecule command
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<molecule>` demonstrating how to set up a small bulk water system for
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SPC/E with rigid bonds.
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.. code-block:: LAMMPS
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units real
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atom_style full
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region box block -5 5 -5 5 -5 5
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create_box 2 box bond/types 1 angle/types 1 &
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extra/bond/per/atom 2 extra/angle/per/atom 1 extra/special/per/atom 2
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mass 1 15.9994
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mass 2 1.008
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pair_style lj/cut/coul/cut 10.0
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pair_coeff 1 1 0.1553 3.166
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pair_coeff 1 2 0.0 1.0
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pair_coeff 2 2 0.0 1.0
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bond_style zero
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bond_coeff 1 1.0
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angle_style zero
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angle_coeff 1 109.47
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molecule water spce.mol
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create_atoms 0 random 33 34564 NULL mol water 25367 overlap 1.33
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timestep 1.0
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fix rigid all shake 0.0001 10 10000 b 1 a 1
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minimize 0.0 0.0 1000 10000
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velocity all create 300.0 5463576
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fix integrate all nvt temp 300.0 300.0 100.0
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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 upto
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write_data spce.data nocoeff
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.. _spce_molecule:
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.. code-block::
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# Water molecule. SPC/E geometry
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3 atoms
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2 bonds
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1 angles
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Coords
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1 0.00000 -0.06461 0.00000
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2 0.81649 0.51275 0.00000
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3 -0.81649 0.51275 0.00000
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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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Charges
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1 -0.8476
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2 0.4238
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3 0.4238
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Bonds
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1 1 1 2
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2 1 1 3
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Angles
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1 1 2 1 3
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Shake Flags
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1 1
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2 1
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3 1
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Shake Atoms
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1 1 2 3
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2 1 2 3
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3 1 2 3
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Shake Bond Types
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1 1 1 1
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2 1 1 1
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3 1 1 1
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Special Bond Counts
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1 2 0 0
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2 1 1 0
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3 1 1 0
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Special Bonds
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1 2 3
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2 1 3
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3 1 2
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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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.. _howto-Berendsen:
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**(Berendsen2)** Berendsen, Grigera, Straatsma, J Phys Chem, 91, 6269-6271 (1987).
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