ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity
Files
f1d19c96cba5fd14c469b6a5a6e36470e5b73aca
lammps/doc/src/Howto_tip4p.rst

395 lines
12 KiB
ReStructuredText
Raw Blame History

TIP4P and OPC water models
==========================
The four-point TIP4P rigid water model extends the traditional
:doc:`three-point TIP3P <Howto_tip3p>` model by adding an additional
site M, usually massless, where the charge associated with the oxygen
atom is placed. This site M is located at a fixed distance away from
the oxygen along the bisector of the HOH bond angle. 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. Very similar to the TIP4P
model is the OPC water model. It can be realized the same way as TIP4P
but has different geometry and force field parameters.
There are two ways to implement TIP4P-like water in LAMMPS:
#. Use a specially written pair style that uses the :ref:`TIP3P geometry
<tip3p_molecule>` without the point M. The point M location is then
implicitly derived from the other atoms or each water molecule and
used during the force computation. The forces on M are then
projected on the oxygen and the two hydrogen atoms. This is
computationally very efficient, but the charge distribution in space
is only correct within the tip4p labeled styles. So all other
computations using charges will "see" the negative charge incorrectly
located on the oxygen atom unless they are specially written for using
the TIP4P geometry internally as well, e.g. :doc:`compute dipole/tip4p
<compute_dipole>`, :doc:`fix efield/tip4p <fix_efield>`, or
:doc:`kspace_style pppm/tip4p <kspace_style>`.
This can be done with the following pair styles for Coulomb with a cutoff:
* :doc:`pair_style tip4p/cut <pair_coul>`
* :doc:`pair_style lj/cut/tip4p/cut <pair_lj_cut_tip4p>`
or these commands for a long-range Coulomb treatment:
* :doc:`pair_style tip4p/long <pair_coul>`
* :doc:`pair_style lj/cut/tip4p/long <pair_lj_cut_tip4p>`
* :doc:`pair_style lj/long/tip4p/long <pair_lj_long>`
* :doc:`pair_style tip4p/long/soft <pair_fep_soft>`
* :doc:`pair_style lj/cut/tip4p/long/soft <pair_fep_soft>`
* :doc:`kspace_style pppm/tip4p <kspace_style>`
* :doc:`kspace_style pppm/disp/tip4p <kspace_style>`
The bond lengths and bond angles should be held fixed using the
:doc:`fix shake <fix_shake>` or :doc:`fix rattle <fix_shake>` command,
unless a parameterization for a flexible TIP4P model is used. The
parameter sets listed below are all for rigid TIP4P model variants and
thus the bond and angle force constants are not used and can be set to
any legal value; only equilibrium length and angle are used.
#. Use an :ref:`explicit 4 point TIP4P geometry <tip4p_molecule>` where
the oxygen atom carries no charge and the M point no Lennard-Jones
interactions. Since :doc:`fix shake <fix_shake>` or :doc:`fix rattle
<fix_shake>` may not be applied to this kind of geometry, :doc:`fix
rigid or fix rigid/small <fix_rigid>` or its thermostatted variants
are required to maintain a rigid geometry. This avoids some of the
issues with respect to analysis and non-tip4p styles, but it is a
more costly force computation (more atoms in the same volume and thus
more neighbors in the neighbor lists) and requires a much shorter
timestep for stable integration of the rigid body motion. Since no
bonds or angles are required, they do not need to be defined and atom
style charge would be sufficient for a bulk TIP4P water system. In
order to avoid that LAMMPS produces an error due to the massless M
site a tiny non-zero mass needs to be assigned.
The table below lists the force field parameters (in real :doc:`units
<units>`) to for a selection of popular variants of the TIP4P model.
There is the rigid TIP4P model with a cutoff :ref:`(Jorgensen)
<Jorgensen5>`, the TIP4/Ice model :ref:`(Abascal1) <Abascal1>`, the
TIP4P/2005 model :ref:`(Abascal2) <Abascal2>` and a version of TIP4P
parameters adjusted for use with a long-range Coulombic solver
(e.g. Ewald or PPPM in LAMMPS). Note that for implicit TIP4P models the
OM distance is specified in the :doc:`pair_style <pair_style>` command,
not as part of the pair coefficients. Also parameters for the OPC
model (:ref:`Izadi <Izadi>`) are provided.
.. list-table::
:header-rows: 1
:widths: 40 12 12 14 11 11
* - Parameter
- TIP4P (original)
- TIP4P/Ice
- TIP4P/2005
- TIP4P (Ewald)
- OPC
* - O mass (amu)
- 15.9994
- 15.9994
- 15.9994
- 15.9994
- 15.9994
* - H mass (amu)
- 1.008
- 1.008
- 1.008
- 1.008
- 1.008
* - O or M charge (:math:`e`)
- -1.040
- -1.1794
- -1.1128
- -1.04844
- -1.3582
* - H charge (:math:`e`)
- 0.520
- 0.5897
- 0.5564
- 0.52422
- 0.6791
* - LJ :math:`\epsilon` of OO (kcal/mole)
- 0.1550
- 0.21084
- 0.1852
- 0.16275
- 0.21280
* - LJ :math:`\sigma` of OO (:math:`\AA`)
- 3.1536
- 3.1668
- 3.1589
- 3.16435
- 3.1660
* - LJ :math:`\epsilon` of HH, MM, OH, OM, HM (kcal/mole)
- 0.0
- 0.0
- 0.0
- 0.0
- 0.0
* - LJ :math:`\sigma` of HH, MM, OH, OM, HM (:math:`\AA`)
- 1.0
- 1.0
- 1.0
- 1.0
- 1.0
* - :math:`r_0` of OH bond (:math:`\AA`)
- 0.9572
- 0.9572
- 0.9572
- 0.9572
- 0.8724
* - :math:`\theta_0` of HOH angle
- 104.52\ :math:`^{\circ}`
- 104.52\ :math:`^{\circ}`
- 104.52\ :math:`^{\circ}`
- 104.52\ :math:`^{\circ}`
- 103.60\ :math:`^{\circ}`
* - OM distance (:math:`\AA`)
- 0.15
- 0.1577
- 0.1546
- 0.1250
- 0.1594
Note that the when using a TIP4P pair style, the neighbor list cutoff
for Coulomb interactions is effectively extended by a distance 2 \* (OM
distance), to account for the offset distance of the fictitious charges
on O atoms in water molecules. Thus, it is typically best in an
efficiency sense to use a LJ cutoff >= Coulomb cutoff + 2\*(OM
distance), to shrink the size of the neighbor list. This leads to
slightly larger cost for the long-range calculation, so you can test the
trade-off for your model. The OM distance and the LJ and Coulombic
cutoffs are set in the :doc:`pair_style lj/cut/tip4p/long
<pair_lj_cut_tip4p>` command.
Below is the code for a LAMMPS input file using the implicit method and
the :ref:`TIP3P molecule file <tip3p_molecule>`. Because the TIP4P
charges are different from TIP3P they need to be reset (or the molecule
file changed). For simplicity and speed the example uses a cutoff
Coulomb. Most production simulations require long-range Coulomb
instead.
.. 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/tip4p/cut 1 2 1 1 0.15 8.0
pair_coeff 1 1 0.1550 3.1536
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 # this uses the TIP3P geometry
create_atoms 0 random 33 34564 NULL mol water 25367 overlap 1.33
# must change charges for TIP4P
set type 1 charge -1.040
set type 2 charge 0.520
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 tip4p-implicit.data nocoeff
When constructing an OPC model, we cannot use the ``tip3p.mol`` file due
to the different geometry. Below is a molecule file providing the 3
sites of an implicit OPC geometry for use with TIP4P styles. Note, that
the "Shake" and "Special" sections are missing here. Those will be
auto-generated by LAMMPS when the molecule file is loaded *after* the
simulation box has been created. These sections are required only when
the molecule file is loaded *before*.
.. _opc3p_molecule:
.. code-block::
# Water molecule. 3 point geometry for OPC model
3 atoms
2 bonds
1 angles
Coords
1 0.00000 -0.06037 0.00000
2 0.68558 0.50250 0.00000
3 -0.68558 0.50250 0.00000
Types
1 1 # O
2 2 # H
3 2 # H
Charges
1 -1.3582
2 0.6791
3 0.6791
Bonds
1 1 1 2
2 1 1 3
Angles
1 1 2 1 3
Below is a LAMMPS input file using the implicit method to implement
the OPC model using the molecule file from above and including the
PPPM long-range Coulomb solver.
.. 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/tip4p/long 1 2 1 1 0.1594 12.0
pair_coeff 1 1 0.2128 3.166
pair_coeff 2 2 0.0 1.0
bond_style zero
bond_coeff 1 0.8724
angle_style zero
angle_coeff 1 103.6
kspace_style pppm/tip4p 1.0e-5
molecule water opc3p.mol # this file has the OPC geometry but is without M
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 opc-implicit.data nocoeff
Below is the code for a LAMMPS input file using the explicit method and
a TIP4P molecule file. Because of using :doc:`fix rigid/small
<fix_rigid>` no bonds need to be defined and thus no extra storage needs
to be reserved for them, but we need to either switch to 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. Also a
:doc:`neigh_modify exclude <neigh_modify>` command is added to exclude
computing intramolecular non-bonded interactions, since those are
removed by the rigid fix anyway:
.. code-block:: LAMMPS
units real
atom_style charge
atom_modify map array
region box block -5 5 -5 5 -5 5
create_box 3 box
mass 1 15.9994
mass 2 1.008
mass 3 1.0e-100
pair_style lj/cut/coul/cut 8.0
pair_coeff 1 1 0.1550 3.1536
pair_coeff 2 2 0.0 1.0
pair_coeff 3 3 0.0 1.0
fix mol all property/atom mol ghost yes
molecule water tip4p.mol
create_atoms 0 random 33 34564 NULL mol water 25367 overlap 1.33
neigh_modify exclude molecule/intra all
timestep 0.5
fix integrate all rigid/small molecule langevin 300.0 300.0 100.0 2345634
thermo_style custom step temp press etotal density pe ke
thermo 2000
run 40000
write_data tip4p-explicit.data nocoeff
.. _tip4p_molecule:
.. code-block::
# Water molecule. Explicit TIP4P geometry for use with fix rigid
4 atoms
Coords
1 0.00000 -0.06556 0.00000
2 0.75695 0.52032 0.00000
3 -0.75695 0.52032 0.00000
4 0.00000 0.08444 0.00000
Types
1 1 # O
2 2 # H
3 2 # H
4 3 # M
Charges
1 0.000
2 0.520
3 0.520
4 -1.040
Wikipedia also has a nice article on `water models <https://en.wikipedia.org/wiki/Water_model>`_.
----------
.. _Jorgensen5:
**(Jorgensen)** Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem
Phys, 79, 926 (1983).
.. _Abascal1:
**(Abascal1)** Abascal, Sanz, Fernandez, Vega, J Chem Phys, 122, 234511 (2005)
https://doi.org/10.1063/1.1931662
.. _Abascal2:
**(Abascal2)** Abascal, J Chem Phys, 123, 234505 (2005)
https://doi.org/10.1063/1.2121687
.. _Izadi:
**(Izadi)** Izadi, Anandakrishnan, Onufriev, J. Phys. Chem. Lett., 5, 21, 3863 (2014)
https://doi.org/10.1021/jz501780a
Reference in New Issue View Git Blame Copy Permalink