From: Sebastian Kehl Date: Wed, 29 Sep 2021 11:44:33 +0000 (+0200) Subject: Update documentation with changed sc-gapsys parameter names. X-Git-Url: http://biod.pnpi.spb.ru/gitweb/?a=commitdiff_plain;h=3e1a6f7b734f249314ff6d3abb22d0e167166f10;p=alexxy%2Fgromacs.git 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 1513744db9..4b624dd1a0 100644 --- 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 ` 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 `. 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 `. 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 cfae901aa0..5077b7db91 100644 --- 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