Overhaul forcefield parameters for ions

.github/workflows/test.yml

@@ -50,6 +50,10 @@ jobs:
           pip install -r requirements.txt
           pip install -r requirements-dev.txt
           pip install -e .
+      - name: Prepare Packmol
+        run: |
+          echo $HOME
+          echo "$HOME/work/mdgo/mdgo/tests/packmol" >> $GITHUB_PATH
       - name: Prepare Selenium
         # https://github.com/marketplace/actions/setup-chromedriver
         uses: nanasess/setup-chromedriver@master

docs/source/aqueous.rst

@@ -0,0 +1,152 @@
+
+================================
+Force Fields for Aqueous Systems
+================================
+
+The Aqueous module provides tools for setting up molecular dynamics simulations
+involving water and ions.
+
+Water Models
+============
+
+`mdgo` contains parameters for several popular water models. This section lists
+a brief description and literature reference to the available models.
+
+SPC
+---
+
+TIP3P-EW
+--------
+
+TIP3P-FB
+--------
+
+Wang, L., Martinez, T. J., Pande, V.S., Building Force Fields: An Automatic, Systematic,
+and Reproducible Approach. J. Phys. Chem. Lett. 2014, 5, 11, 1885–1891.
+https://pubs.acs.org/doi/abs/10.1021/jz500737m
+
+Parameters are given in Supporting Table 1. Note that the epsilon for Oxygen must be converted
+from kJ/mol to kcal/mol.
+
+TIP4P-EW
+--------
+
+[Vega & de Miguel, J Chem Phys 126:154707 (2007), Vega et al, Faraday Discuss 141:251 (2009)].
+
+TIP4P-FB
+--------
+
+Wang, L., Martinez, T. J., Pande, V.S., Building Force Fields: An Automatic, Systematic,
+and Reproducible Approach. J. Phys. Chem. Lett. 2014, 5, 11, 1885–1891.
+https://pubs.acs.org/doi/abs/10.1021/jz500737m
+
+Parameters are given in Supporting Table 1. Note that the epsilon for oxygen must be converted
+from kJ/mol to kcal/mol.
+
+TIP4P-2005
+----------
+
+Abascal & Vega, J Chem Phys 123:234505 (2005)
+
+OPC
+----
+
+Izadi, Anandakrishnan, and Onufriev, Building Water Models: A Different Approach. 
+J. Phys. Chem. Lett. 2014, 5, 21, 3863–3871 https://doi.org/10.1021/jz501780a
+
+Parameters are given in Table 2. Note that the epsilon for oxygen must be converted
+from kJ/mol to kcal/mol.
+
+OPC3
+----
+
+Izadi and Onufriev, Accuracy limit of rigid 3-point water models
+J. Chemical Physics 145, 074501, 2016. https://doi.org/10.1063/1.4960175
+
+Parameters are given in Table II. Note that the epsilon for oxygen must be converted
+from kJ/mol to kcal/mol.
+
+
+Ion Parameter Sets
+==================
+
+``mdgo`` contains a compilation of several sets of Lennard Jones
+parameters for ions in water. All values are reported as :math:`\sigma_i`
+and :math:`\epsilon_i` in the equation
+
+.. math::
+
+   E = 4 \\epsilon_i \\left[ \\left( \\frac{\sigma_i}{r} \\right)^{12} - \\left( \\frac{\sigma_i}{r} \\right)^{6} \\right]
+
+Values of :math:`\sigma_i` and :math:`\epsilon_i` are given in Angstrom
+and kcal/mol, respectively, corresponding to the ‘real’ units system in
+LAMMPS.
+
+Aqvist (aq)
+-----------
+
+Aqvist, J. Ion-Water Interaction Potentials Derived from Free Energy
+Perturbation Slmulations J. Phys. Chem. 1990, 94, 8021– 8024.
+https://pubs.acs.org/doi/10.1021/j100384a009
+
+Values were parameterized to the SPC water model and are reported in
+Table I and II as :math:`A_i` and :math:`B_i` coefficients in the
+following form of the Lennard-Jones potential:
+
+.. math::
+
+
+   E = \left[ \left( \frac{A_i^2}{r} \right)^{12} - \left( \frac{B_i^2}{r} \right)^{6} \right]
+
+This parameter set is a work in progress!
+
+Jensen and Jorgensen (jj)
+-------------------------
+
+Jensen, K. P. and Jorgensen, W. L., Halide, Ammonium, and Alkali Metal
+Ion Parameters for Modeling Aqueous Solutions. J. Chem. Theory Comput.
+2006, 2, 6, 1499–1509. https://pubs.acs.org/doi/abs/10.1021/ct600252r
+
+Values were parameterized to the TIP4P water model using geometric
+combining rules and are reported directly as sigma_i and epsilon_i in
+Table 2.
+
+Joung-Cheatham (jc)
+-------------------
+
+Joung, and Thomas E. Cheatham, Thomas E. III, Determination of Alkali
+and Halide Monovalent Ion Parameters for Use in Explicitly Solvated
+Biomolecular Simulations. J. Phys. Chem. B 2008, 112, 30, 9020–9041.
+https://pubs.acs.org/doi/10.1021/jp8001614
+
+Values were parameterized for the SPC/E, TIP3P, and TIP4P_EW water
+models using Lorentz-Berthelot combining rules (LAMMPS: ‘arithmetic’)
+and are reported in Table 5 as :math:`R_{min}`/2 and epsilon_i. R_min/2
+values are converted to :math:`\sigma_i` values using
+:math:`\sigma_i = R_{min}/2 * 2^(5/6)`
+
+Li and Merz group (lm)
+----------------------
+
+Sengupta et al. Parameterization of Monovalent Ions for the OPC3, OPC,
+TIP3P-FB, and TIP4P-FB Water Models. J. Chem. Information Modeling
+61(2), 2021. https://pubs.acs.org/doi/10.1021/acs.jcim.0c01390
+
+Li et al. Systematic Parametrization of Divalent Metal Ions for the
+OPC3, OPC, TIP3P-FB, and TIP4P-FB Water Models. J. Chem. Theory and
+Computation 16(7), 2020.
+https://pubs.acs.org/doi/10.1021/acs.jctc.0c00194
+
+Li et al. Parametrization of Trivalent and Tetravalent Metal Ions for
+the OPC3, OPC, TIP3P-FB, and TIP4P-FB Water Models. J. Chem. Theory and
+Computation 17(4), 2021.
+https://pubs.acs.org/doi/10.1021/acs.jctc.0c01320
+
+Values were parameterized for the OPC, OPC3, TIP3P-FB, and TIP4P-FB
+water models using Lorentz-Berthelot combining rules (LAMMPS:
+‘arithmetic’) and are reported in Table 3 as :math:`R_{min}`/2 and
+epsilon_i. R_min/2 values are converted to :math:`\sigma_i` values using
+:math:`\sigma_i = R_{min}/2 * 2^(5/6)`. This set of values is optimized
+for reproducing ion-oxygen distance. An alternate set of values optimized for
+hydration free energies is available in the original papers.
+