continue refactoring for bio force field and water moldel discussions

doc/src/Howto.rst

@@ -66,6 +66,7 @@ Force fields howto
    :name: force_howto
    :maxdepth: 1
 
+   Howto_FFgeneral
    Howto_bioFF
    Howto_amoeba
    Howto_tip3p

doc/src/Howto_FFgeneral.rst

@@ -0,0 +1,55 @@
+Some general force field considerations
+=======================================
+
+A compact summary of the concepts, definitions, and properties of force
+fields with explicit bonded interactions (like the ones discussed in
+this HowTo) is given in :ref:`(Gissinger) <Typelabel2>`.
+
+A force field has 2 parts: the formulas that define its potential
+functions and the coefficients used for a particular system.  To assign
+parameters it is first required to assign atom types.  Those are not
+only based on the elements, but also on the chemical environment due to
+the atoms bound to them.  This often follows the chemical concept of
+*functional groups*.  Example: a carbon atom bound with a single bond to
+a single OH-group (alcohol) would be a different atom type than a carbon
+atom bound to a methyl CH3 group (aliphatic carbon).  The atom types
+usually then determine the non-bonded Lennard-Jones parameters and the
+parameters for bonds, angles, dihedrals, and impropers.  On top of that,
+partial charges have to be applied.  Those are usually independent of
+the atom types and are determined either for groups of atoms called
+residues with some fitting procedure based on quantum mechanical
+calculations, or based on some increment system that add or subtract
+increments from the partial charge of an atom based on the types of
+the neighboring atoms.
+
+Force fields differ in the strategies they employ to determine the
+parameters and charge distribution in how generic or specific they are
+which in turn has an impact on the accuracy (compare for example
+CGenFF to CHARMM and GAFF to Amber).  Because of the different
+strategies, it is not a good idea to use a mix of parameters from
+different force field *families* (like CHARMM, Amber, or GROMOS)
+and that extends to the parameters for the solvent, especially
+water.  The publication describing the parameterization of a force
+field will describe which water model to use.  Changing the water
+model usually leads to overall worse results (even if it may improve
+on the water itself).
+
+In addition, one has to consider that *families* of force fields like
+CHARMM, Amber, OPLS, or GROMOS have evolved over time and thus provide
+different *revisions* of the force field parameters.  These often
+corresponds to changes in the functional form or the parameterization
+strategies.  This may also result in changes required for simulation
+settings like the preferred cutoff or how Coulomb interactions are
+computed (cutoff, smoothed/shifted cutoff, or long-range with Ewald
+summation or equivalent).  Unless explicitly stated in the publication
+describing the force field, the Coulomb interaction cannot be chosen at
+will but must match the revision of the force field.  That said,
+liberties may be taken during the initial equilibration of a system to
+speed up the process, but not for production simulations.
+
+----------
+
+.. _Typelabel2:
+
+**(Gissinger)** J. R. Gissinger, I. Nikiforov, Y. Afshar, B. Waters, M. Choi, D. S. Karls, A. Stukowski, W. Im, H. Heinz, A. Kohlmeyer, and E. B. Tadmor, J Phys Chem B, 128, 3282-3297 (2024).
+

doc/src/Howto_bioFF.rst

@@ -1,22 +1,16 @@
 CHARMM, AMBER, COMPASS, DREIDING, and OPLS force fields
 =======================================================
 
-A compact summary of the concepts, definitions, and properties of
+Here we only discuss formulas implemented in LAMMPS that correspond to
-force fields with explicit bonded interactions (like the ones discussed
+formulas commonly used in the CHARMM, AMBER, COMPASS, and DREIDING force
-in this HowTo) is given in :ref:`(Gissinger) <Typelabel2>`.
+fields.  Setting coefficients is done either from special sections in an
-
+input data file via the :doc:`read_data <read_data>` command or in the
-A force field has 2 parts: the formulas that define it and the
+input script with commands like :doc:`pair_coeff <pair_coeff>` or
-coefficients used for a particular system.  Here we only discuss
+:doc:`bond_coeff <bond_coeff>` and so on.  See the :doc:`Tools <Tools>`
-formulas implemented in LAMMPS that correspond to formulas commonly used
+doc page for additional tools that can use CHARMM, AMBER, or Materials
-in the CHARMM, AMBER, COMPASS, and DREIDING force fields.  Setting
+Studio generated files to assign force field coefficients and convert
-coefficients is done either from special sections in an input data file
+their output into LAMMPS input. LAMMPS input scripts can also be
-via the :doc:`read_data <read_data>` command or in the input script with
+generated by `charmm-gui.org <https://charmm-gui.org/>`_.
-commands like :doc:`pair_coeff <pair_coeff>` or :doc:`bond_coeff
-<bond_coeff>` and so on.  See the :doc:`Tools <Tools>` doc page for
-additional tools that can use CHARMM, AMBER, or Materials Studio
-generated files to assign force field coefficients and convert their
-output into LAMMPS input. LAMMPS input scripts can also be generated by
-`charmm-gui.org <https://charmm-gui.org/>`_.
 
 CHARMM and AMBER
 ----------------
@@ -203,9 +197,11 @@ rather than individual force constants and geometric parameters that
 depend on the particular combinations of atoms involved in the bond,
 angle, or torsion terms.  DREIDING has an :doc:`explicit hydrogen bond
 term <pair_hbond_dreiding>` to describe interactions involving a
-hydrogen atom on very electronegative atoms (N, O, F).  Unlike CHARMM
+hydrogen atom on very electronegative atoms (N, O, F).  Unlike CHARMM or
-or AMBER, the DREIDING force field has not been parameterized for
+AMBER, the DREIDING force field has not been parameterized for
-considering solvents (like water).
+considering solvents (like water) and has no rules for assigning
+(partial) charges.  That will seriously limit its accuracy when used for
+simulating systems where those matter.
 
 See :ref:`(Mayo) <howto-Mayo>` for a description of the DREIDING force field
 
@@ -272,10 +268,6 @@ compatible with a subset of OPLS interactions.
 
 ----------
 
-.. _Typelabel2:
-
-**(Gissinger)** J. R. Gissinger, I. Nikiforov, Y. Afshar, B. Waters, M. Choi, D. S. Karls, A. Stukowski, W. Im, H. Heinz, A. Kohlmeyer, and E. B. Tadmor, J Phys Chem B, 128, 3282-3297 (2024).
-
 .. _howto-MacKerell:
 
 **(MacKerell)** MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field, Fischer, Gao, Guo, Ha, et al (1998).  J Phys Chem, 102, 3586 . https://doi.org/10.1021/jp973084f

doc/src/Howto_spc.rst

@@ -1,5 +1,5 @@
-SPC water model
+SPC and SPC/E water model
-===============
+=========================
 
 The SPC water model specifies a 3-site rigid water molecule with
 charges and Lennard-Jones parameters assigned to each of the three atoms.

doc/src/Howto_tip4p.rst

@@ -212,11 +212,11 @@ file changed):
 
 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 for an implicit OPC geometry with TIP4P styles.  Note, that the
+sites of an implicit OPC geometry for use with TIP4P styles.  Note, that
-"Shake" and "Special" sections are missing here.  Those will be
+the "Shake" and "Special" sections are missing here.  Those will be
-auto-generated since the molecule file is loaded *after* the simulation
+auto-generated by LAMMPS when the molecule file is loaded *after* the
-box has been created. They are required only when the molecule file
+simulation box has been created.  These sections are required only when
-is loaded *before*.
+the molecule file is loaded *before*.
 
 .. _opc3p_molecule:
 .. code-block::