add information about the OPC model to the TIP4P howto
This commit is contained in:
Axel Kohlmeyer
@ -1,5 +1,5 @@
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TIP4P water model
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=================
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TIP4P and OPC water models
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==========================
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The four-point TIP4P rigid water model extends the traditional
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:doc:`three-point TIP3P <Howto_tip3p>` model by adding an additional
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@ -9,9 +9,11 @@ the oxygen along the bisector of the HOH bond angle. A bond style of
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:doc:`harmonic <bond_harmonic>` and an angle style of :doc:`harmonic
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<angle_harmonic>` or :doc:`charmm <angle_charmm>` should also be used.
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In case of rigid bonds also bond style :doc:`zero <bond_zero>` and angle
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style :doc:`zero <angle_zero>` can be used.
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style :doc:`zero <angle_zero>` can be used. Very similar to the TIP4P
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model is the OPC water model. It can be realized the same way as TIP4P
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but has different geometry and force field parameters.
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There are two ways to implement TIP4P water in LAMMPS:
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There are two ways to implement TIP4P-like water in LAMMPS:
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#. Use a specially written pair style that uses the :ref:`TIP3P geometry
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<tip3p_molecule>` without the point M. The point M location is then
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@ -21,7 +23,10 @@ There are two ways to implement TIP4P water in LAMMPS:
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computationally very efficient, but the charge distribution in space
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is only correct within the tip4p labeled styles. So all other
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computations using charges will "see" the negative charge incorrectly
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on the oxygen atom.
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located on the oxygen atom unless they are specially written for using
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the TIP4P geometry internally as well, e.g. :doc:`compute dipole/tip4p
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<compute_dipole>`, :doc:`fix efield/tip4p <fix_efield>`, or
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:doc:`kspace_style pppm/tip4p <kspace_style>`.
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This can be done with the following pair styles for Coulomb with a cutoff:
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@ -68,77 +73,90 @@ TIP4P/2005 model :ref:`(Abascal2) <Abascal2>` and a version of TIP4P
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parameters adjusted for use with a long-range Coulombic solver
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(e.g. Ewald or PPPM in LAMMPS). Note that for implicit TIP4P models the
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OM distance is specified in the :doc:`pair_style <pair_style>` command,
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not as part of the pair coefficients.
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not as part of the pair coefficients. Also parameters for the OPC
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model (:ref:`Izadi <Izadi>`) are provided.
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.. list-table::
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:header-rows: 1
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:widths: 36 19 13 15 17
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:widths: 40 12 12 14 11 11
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* - Parameter
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- TIP4P (original)
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- TIP4P/Ice
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- TIP4P/2005
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- TIP4P (Ewald)
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- OPC
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* - O mass (amu)
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- 15.9994
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- 15.9994
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- 15.9994
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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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- 1.008
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- 1.008
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- 1.008
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* - O or M charge (:math:`e`)
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- -1.040
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- -1.1794
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- -1.1128
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- -1.04844
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- -1.3582
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* - H charge (:math:`e`)
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- 0.520
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- 0.5897
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- 0.5564
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- 0.52422
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- 0.6791
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* - LJ :math:`\epsilon` of OO (kcal/mole)
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- 0.1550
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- 0.21084
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- 0.1852
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- 0.16275
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- 0.21280
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* - LJ :math:`\sigma` of OO (:math:`\AA`)
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- 3.1536
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- 3.1668
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- 3.1589
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- 3.16435
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- 3.1660
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* - LJ :math:`\epsilon` of HH, MM, OH, OM, HM (kcal/mole)
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- 0.0
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- 0.0
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- 0.0
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- 0.0
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- 0.0
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* - LJ :math:`\sigma` of HH, MM, OH, OM, HM (:math:`\AA`)
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- 1.0
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- 1.0
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- 1.0
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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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- 0.9572
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- 0.9572
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- 0.8724
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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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- 104.52\ :math:`^{\circ}`
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- 104.52\ :math:`^{\circ}`
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- 103.60\ :math:`^{\circ}`
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* - OM distance (:math:`\AA`)
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- 0.15
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- 0.1577
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- 0.1546
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- 0.1250
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- 0.1594
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Note that the when using the TIP4P pair style, the neighbor list cutoff
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Note that the when using a TIP4P pair style, the neighbor list cutoff
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for Coulomb interactions is effectively extended by a distance 2 \* (OM
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distance), to account for the offset distance of the fictitious charges
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on O atoms in water molecules. Thus it is typically best in an
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on O atoms in water molecules. Thus, it is typically best in an
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efficiency sense to use a LJ cutoff >= Coulomb cutoff + 2\*(OM
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distance), to shrink the size of the neighbor list. This leads to
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slightly larger cost for the long-range calculation, so you can test the
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@ -192,6 +210,94 @@ file changed):
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run 20000
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write_data tip4p-implicit.data nocoeff
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When constructing an OPC model, we cannot use the ``tip3p.mol`` file due
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to the different geometry. Below is a molecule file providing the 3
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sites for an implicit OPC geometry with TIP4P styles. Note, that the
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"Shake" and "Special" sections are missing here. Those will be
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auto-generated since the molecule file is loaded *after* the simulation
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box has been created. They are required only when the molecule file
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is loaded *before*.
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.. _opc3p_molecule:
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.. code-block::
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# Water molecule. 3 point geometry for OPC model
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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 -0.06037 0.00000
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2 0.68558 0.50250 0.00000
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3 -0.68558 0.50250 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 -1.3582
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2 0.6791
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3 0.6791
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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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Below is a LAMMPS input file using the implicit method to implement
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the OPC model using the molecule file from above and including the
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PPPM long-range Coulomb solver.
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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/tip4p/long 1 2 1 1 0.1594 12.0
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pair_coeff 1 1 0.2128 3.166
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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 0.8724
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angle_style zero
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angle_coeff 1 103.6
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kspace_style pppm/tip4p 1.0e-5
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molecule water opc3p.mol # this file has the OPC geometry but is without M
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create_atoms 0 random 33 34564 NULL mol water 25367 overlap 1.33
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fix rigid all shake 0.001 10 10000 b 1 a 1
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minimize 0.0 0.0 1000 10000
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reset_timestep 0
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timestep 1.0
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velocity all create 300.0 5463576
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fix integrate all nvt temp 300 300 100.0
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thermo_style custom step temp press etotal pe
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thermo 1000
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run 20000
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write_data opc-implicit.data nocoeff
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Below is the code for a LAMMPS input file using the explicit method and
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a TIP4P molecule file. Because of using :doc:`fix rigid/small
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<fix_rigid>` no bonds need to be defined and thus no extra storage needs
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@ -279,3 +385,8 @@ Phys, 79, 926 (1983).
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**(Abascal2)** Abascal, J Chem Phys, 123, 234505 (2005)
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https://doi.org/10.1063/1.2121687
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.. _Izadi:
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**(Izadi)** Izadi, Anandakrishnan, Onufriev, J. Phys. Chem. Lett., 5, 21, 3863 (2014)
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https://doi.org/10.1021/jz501780a
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@ -103,6 +103,7 @@ Amit
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amsmath
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amu
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Amzallag
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Anandakrishnan
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analytical
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Anders
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Andric
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@ -1732,6 +1733,7 @@ Iyz
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iz
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izcm
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ized
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Izadi
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Izrailev
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Izumi
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Izvekov
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@ -2808,6 +2810,7 @@ oneMKL
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oneway
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onlysalt
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ons
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Onufriev
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OO
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Oord
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opencl
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