From: Rossen Apostolov Date: Thu, 12 Jun 2014 15:03:10 +0000 (+0200) Subject: Added a note about sc-coul being auto turned on. X-Git-Url: http://biod.pnpi.spb.ru/gitweb/?a=commitdiff_plain;h=262bf922dec01ec0e0e284d656189cec476e4f33;p=alexxy%2Fgromacs.git 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 13e7e6b33b..04658152e2 100644 --- 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 f0fa212a60..1d6fd0f53e 100644 --- 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.
sc-r-power: (6)
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).
sc-coul: (no)
-
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.
+
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 couple-lambda0/couple-lambda1, and you can still turn off soft-core +interactions by setting sc-alpha=0.
sc-power: (0)
the power for lambda in the soft-core function, only the values 1 and 2 are supported
sc-sigma: (0.3) [nm]