Update documentation with changed sc-gapsys parameter names.

diff --git a/docs/reference-manual/functions/free-energy-interactions.rst b/docs/reference-manual/functions/free-energy-interactions.rst
index 1513744db9ad15444da744ccb194d51756cfbc98..4b624dd1a0af63fc4b62d2f7a3fbe808c3affb3d 100644 (file)
--- a/docs/reference-manual/functions/free-energy-interactions.rst
+++ b/docs/reference-manual/functions/free-energy-interactions.rst
@@ -338,10 +338,10 @@ the soft-cored non-bonded interactions using the formalism by Gapsys *et al.*\ :
 The Gapsys *et al.* soft-core is formulated to act on the level of van der Waals and electrostatic forces:
 the non-bonded interactions are linearized at a point defined as, :math:`r_{scLJ}` or :math:`r_{scQ}`, respectively.
 The linearization point depends on the state of the system as controlled by the :math:`\lambda` parameter and 
-two parameters :math:`\alpha_Q` (set with ``sc-scale-linpoint-Q-gapsys``) and :math:`\alpha_{LJ}` (set with ``sc-scale-linpoint-LJ-gapsys``).
+two parameters :math:`\alpha_Q` (set with ``sc-gapsys-scale-linpoint-Q``) and :math:`\alpha_{LJ}` (set with ``sc-gapsys-scale-linpoint-LJ``).
 The dependence on :math:`\lambda` guarantees that the end-states are properly represented by their hard-core potentials.
 :numref:`Fig. %s <fig-gapsyssc>` illustrates the behaviour of the linearization point, forces and integrated potential energies with respect
-to the parameters :math:`\alpha_Q` and :math:`\alpha_{LJ}`. The optimal choices of the parameter values have been systematically explored in :ref:`185 <refGapsys2012>`. These recommended values are set by default when ``sc-function=gapsys`` is selected: ``sc-scale-linpoint-Q-gapsys=0.3`` and ``sc-scale-linpoint-LJ-gapsys=0.85``.
+to the parameters :math:`\alpha_Q` and :math:`\alpha_{LJ}`. The optimal choices of the parameter values have been systematically explored in :ref:`185 <refGapsys2012>`. These recommended values are set by default when ``sc-function=gapsys`` is selected: ``sc-gapsys-scale-linpoint-Q=0.3`` and ``sc-gapsys-scale-linpoint-LJ=0.85``.
 
 .. _fig-gapsyssc:
 

diff --git a/docs/user-guide/mdp-options.rst b/docs/user-guide/mdp-options.rst
index cfae901aa0eb259f7e039fba8d3ca623b905e3bc..5077b7db9180aced2378a47a607f69487e440c86 100644 (file)
--- a/docs/user-guide/mdp-options.rst
+++ b/docs/user-guide/mdp-options.rst
@@ -2584,7 +2584,7 @@ Free energy calculations
    than :mdp:`sc-sigma`.
    Used only with `sc-function=beutler`
 
-.. mdp:: sc-linpoint-LJ-gapsys
+.. mdp:: sc-gapsys-scale-linpoint-LJ
 
    (0.85)
    for `sc-function=gapsys` it is the unitless alphaLJ parameter.
@@ -2594,7 +2594,7 @@ Free energy calculations
    van der Waals interactions.
    Used only with `sc-function=gapsys`
 
-.. mdp:: sc-linpoint-Q-gapsys
+.. mdp:: sc-gapsys-scale-linpoint-Q
 
    (0.3) [nm/e^2]
    For `sc-function=gapsys` the alphaQ parameter
@@ -2603,7 +2603,7 @@ Free energy calculations
    result in the standard hard-core Coulombic interactions.
    Used only with `sc-function=gapsys`
 
-.. mdp:: sc-sigma-LJ-gapsys
+.. mdp:: sc-gapsys-sigma-LJ
 
    (0.3) [nm]
    for `sc-function=gapsys` the soft-core sigma for particles