227 lines
5.1 KiB
ReStructuredText
227 lines
5.1 KiB
ReStructuredText
TIP3P water model
|
|
=================
|
|
|
|
The TIP3P water model as implemented in CHARMM :ref:`(MacKerell)
|
|
<howto-tip3p>` specifies a 3-site rigid water molecule with charges and
|
|
Lennard-Jones parameters assigned to each of the 3 atoms.
|
|
|
|
A suitable pair style with cutoff Coulomb would be:
|
|
|
|
* :doc:`pair_style lj/cut/coul/cut <pair_lj_cut_coul>`
|
|
|
|
or these commands 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:`kspace_style pppm/disp <kspace_style>`
|
|
|
|
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
|
|
of :doc:`harmonic <bond_harmonic>` and an angle style of :doc:`harmonic
|
|
<angle_harmonic>` or :doc:`charmm <angle_charmm>` should also be used.
|
|
In case of rigid bonds also bond style :doc:`zero <bond_zero>` and angle
|
|
style :doc:`zero <angle_zero>` can be used.
|
|
|
|
The table below lists the force field parameters (in real :doc:`units
|
|
<units>`) to for the water molecule atoms to run a rigid or flexible
|
|
TIP3P-CHARMM model with a cutoff, the original 1983 TIP3P model
|
|
:ref:`(Jorgensen) <Jorgensen1>`, or a TIP3P model with parameters
|
|
optimized for a long-range Coulomb solver (e.g. Ewald or PPPM in LAMMPS)
|
|
:ref:`(Price) <Price1>`. The K values can be used if a flexible TIP3P
|
|
model (without fix shake) is desired, for rigid bonds/angles they are
|
|
ignored.
|
|
|
|
.. list-table::
|
|
:header-rows: 1
|
|
:widths: auto
|
|
|
|
* - Parameter
|
|
- TIP3P-CHARMM
|
|
- TIP3P (original)
|
|
- TIP3P (Ewald)
|
|
* - O mass (amu)
|
|
- 15.9994
|
|
- 15.9994
|
|
- 15.9994
|
|
* - H mass (amu)
|
|
- 1.008
|
|
- 1.008
|
|
- 1.008
|
|
* - O charge (:math:`e`)
|
|
- -0.834
|
|
- -0.834
|
|
- -0.834
|
|
* - H charge (:math:`e`)
|
|
- 0.417
|
|
- 0.417
|
|
- 0.417
|
|
* - LJ :math:`\epsilon` of OO (kcal/mole)
|
|
- 0.1521
|
|
- 0.1521
|
|
- 0.1020
|
|
* - LJ :math:`\sigma` of OO (:math:`\AA`)
|
|
- 3.1507
|
|
- 3.1507
|
|
- 3.188
|
|
* - LJ :math:`\epsilon` of HH (kcal/mole)
|
|
- 0.0460
|
|
- 0.0
|
|
- 0.0
|
|
* - LJ :math:`\sigma` of HH (:math:`\AA`)
|
|
- 0.4
|
|
- 1.0
|
|
- 1.0
|
|
* - LJ :math:`\epsilon` of OH (kcal/mole)
|
|
- 0.0836
|
|
- 0.0
|
|
- 0.0
|
|
* - LJ :math:`\sigma` of OH (:math:`\AA`)
|
|
- 1.7753
|
|
- 1.0
|
|
- 1.0
|
|
* - K of OH bond (kcal/mole/:math:`\AA^2`)
|
|
- 450
|
|
- 450
|
|
- 450
|
|
* - :math:`r_0` of OH bond (:math:`\AA`)
|
|
- 0.9572
|
|
- 0.9572
|
|
- 0.9572
|
|
* - K of HOH angle (kcal/mole)
|
|
- 55.0
|
|
- 55.0
|
|
- 55.0
|
|
* - :math:`\theta_0` of HOH angle
|
|
- 104.52\ :math:`^{\circ}`
|
|
- 104.52\ :math:`^{\circ}`
|
|
- 104.52\ :math:`^{\circ}`
|
|
|
|
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
|
|
<molecule>` demonstrating how to set up a small bulk water system for
|
|
TIP3P with rigid bonds.
|
|
|
|
.. code-block:: LAMMPS
|
|
|
|
units real
|
|
atom_style full
|
|
region box block -5 5 -5 5 -5 5
|
|
create_box 2 box bond/types 1 angle/types 1 &
|
|
extra/bond/per/atom 2 extra/angle/per/atom 1 extra/special/per/atom 2
|
|
|
|
mass 1 15.9994
|
|
mass 2 1.008
|
|
|
|
pair_style lj/cut/coul/cut 8.0
|
|
pair_coeff 1 1 0.1521 3.1507
|
|
pair_coeff 2 2 0.0 1.0
|
|
|
|
bond_style zero
|
|
bond_coeff 1 0.9574
|
|
|
|
angle_style zero
|
|
angle_coeff 1 104.52
|
|
|
|
molecule water tip3p.mol
|
|
create_atoms 0 random 33 34564 NULL mol water 25367 overlap 1.33
|
|
|
|
fix rigid all shake 0.001 10 10000 b 1 a 1
|
|
minimize 0.0 0.0 1000 10000
|
|
|
|
reset_timestep 0
|
|
timestep 1.0
|
|
velocity all create 300.0 5463576
|
|
fix integrate all nvt temp 300 300 100.0
|
|
|
|
thermo_style custom step temp press etotal pe
|
|
|
|
thermo 1000
|
|
run 20000
|
|
write_data tip3p.data nocoeff
|
|
|
|
.. _tip3p_molecule:
|
|
.. code-block::
|
|
|
|
# Water molecule. TIP3P geometry
|
|
|
|
3 atoms
|
|
2 bonds
|
|
1 angles
|
|
|
|
Coords
|
|
|
|
1 0.00000 -0.06556 0.00000
|
|
2 0.75695 0.52032 0.00000
|
|
3 -0.75695 0.52032 0.00000
|
|
|
|
Types
|
|
|
|
1 1 # O
|
|
2 2 # H
|
|
3 2 # H
|
|
|
|
Charges
|
|
|
|
1 -0.834
|
|
2 0.417
|
|
3 0.417
|
|
|
|
Bonds
|
|
|
|
1 1 1 2
|
|
2 1 1 3
|
|
|
|
Angles
|
|
|
|
1 1 2 1 3
|
|
|
|
Shake Flags
|
|
|
|
1 1
|
|
2 1
|
|
3 1
|
|
|
|
Shake Atoms
|
|
|
|
1 1 2 3
|
|
2 1 2 3
|
|
3 1 2 3
|
|
|
|
Shake Bond Types
|
|
|
|
1 1 1 1
|
|
2 1 1 1
|
|
3 1 1 1
|
|
|
|
Special Bond Counts
|
|
|
|
1 2 0 0
|
|
2 1 1 0
|
|
3 1 1 0
|
|
|
|
Special Bonds
|
|
|
|
1 2 3
|
|
2 1 3
|
|
3 1 2
|
|
|
|
|
|
Wikipedia also has a nice article on `water models <https://en.wikipedia.org/wiki/Water_model>`_.
|
|
|
|
----------
|
|
|
|
.. _howto-tip3p:
|
|
|
|
**(MacKerell)** MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
|
|
Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).
|
|
|
|
.. _Jorgensen1:
|
|
|
|
**(Jorgensen)** Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem
|
|
Phys, 79, 926 (1983).
|
|
|
|
.. _Price1:
|
|
|
|
**(Price)** Price and Brooks, J Chem Phys, 121, 10096 (2004).
|