Added a note about sc-coul being auto turned on.

The documentation didn't mention that the soft-core potential
is automatically switched on in the case of a single component
lambda.

Fixes #1421.

Change-Id: Ic478b8b1a68c9ef08764946337f72008808bb2b3

diff --git a/docs/manual/forcefield.tex b/docs/manual/forcefield.tex
index 13e7e6b33ba8271ba2ba8d148213c832a2e15e6e..04658152e28a626e44cf511a9385690efcb2de62 100644 (file)
--- a/docs/manual/forcefield.tex
+++ b/docs/manual/forcefield.tex
@@ -1,7 +1,7 @@
 %
 % This file is part of the GROMACS molecular simulation package.
 %
-% Copyright (c) 2013,2014, by the GROMACS development team, led by
+% Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
 % Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
 % and including many others, as listed in the AUTHORS file in the
 % top-level source directory and at http://www.gromacs.org.
@@ -1880,14 +1880,17 @@ and close to 0 and/or 1 with $p=2$. Lowering {\tt\mbox{sc-sigma}} will decrease
 this effect, but it will also increase the interactions with hydrogens
 relative to the other interactions in the soft-core state.
 
-When soft core potentials are selected (by setting {\tt sc-alpha} \textgreater
+When soft-core potentials are selected (by setting {\tt sc-alpha} \textgreater
 0), and the Coulomb and Lennard-Jones potentials are turned on or off
 sequentially, then the Coulombic interaction is turned off linearly,
-rather than using soft core interactions, which should be less
-statistically noisy in most cases.  This behavior can be overwritten
-by using the mdp option {\tt sc-coul} to {\tt yes}. Additionally, the
-soft-core interaction potential is only applied when either the A or B
-state has zero interaction potential.  If both A and B states have
+rather than using soft-core interactions, which should be less
+statistically noisy in most cases. This behavior can be overwritten
+by using the mdp option {\tt sc-coul} to {\tt yes}. Note that the {\tt sc-coul}
+is only taken into account when lambda states are used, not with
+{\tt couple-lambda0/couple-lambda1}, and you can still turn off soft-core
+interactions by setting {\tt sc-alpha=0}. Additionally, the soft-core
+interaction potential is only applied when either the A or B
+state has zero interaction potential. If both A and B states have
 nonzero interaction potential, default linear scaling described above
 is used. When both Coulombic and Lennard-Jones interactions are turned
 off simultaneously, a soft-core potential is used, and a hydrogen is

diff --git a/docs/old-html/online/mdp_opt.html b/docs/old-html/online/mdp_opt.html
index f0fa212a606c3e4f5963e0171440304271ac2aa9..1d6fd0f53e389ef669fad3a6689677774845f68a 100644 (file)
--- a/docs/old-html/online/mdp_opt.html
+++ b/docs/old-html/online/mdp_opt.html
@@ -1574,8 +1574,10 @@ of 1 is sufficient, while for MBAR -1 should be used.</dd>
 <dt><b>sc-r-power: (6)</b></dt>
 <dd>the power of the radial term in the soft-core equation.  Possible values are 6 and 48. 6 is more standard, and is the default.  When 48 is used, then sc-alpha should generally be much lower (between 0.001 and 0.003).</dd>
 <dt><b>sc-coul: (no)</b></dt>
-<dd>Whether to apply the soft core free energy interaction transformation to the Columbic interaction of a molecule. Default is no, as it is generally
-more efficient to turn off the Coulomic interactions linearly before turning off the van der Waals interactions.</dd>
+<dd>Whether to apply the soft-core free energy interaction transformation to the Columbic interaction of a molecule. Default is no, as it is generally
+more efficient to turn off the Coulomic interactions linearly before turning off the van der Waals interactions. Note that it is only taken into account 
+when lambda states are used, not with <b>couple-lambda0/couple-lambda1</b>, and you can still turn off soft-core 
+interactions by setting <b>sc-alpha=0</b>.</dd>
 <dt><b>sc-power: (0)</b></dt>
 <dd>the power for lambda in the soft-core function, only the values 1 and 2 are supported</dd>
 <dt><b>sc-sigma: (0.3) [nm]</b></dt>