%
% 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.
\beq
d_g(\ve{r}_i;\ve{R}_i) = |\ve{r}_i-\ve{R}_i|
\eeq
-{\bfseries Cylinder} ($g=2$): The particle is kept in a cylinder of given radius
-parallel to the $z$-axis. The force from the flat-bottomed potential acts
-towards the axis of the cylinder. The $z$-component of the force is zero.
+{\bfseries Cylinder} ($g=6,7,8$): The particle is kept in a cylinder of given radius
+parallel to the $x$ ($g=6$), $y$ ($g=7$), or $z$-axis ($g=8$). For backwards compatibility, setting
+$g=2$ is mapped to $g=8$ in the code so that old {\tt .tpr} files and topologies work.
+The force from the flat-bottomed potential acts towards the axis of the cylinder.
+The component of the force parallel to the cylinder axis is zero.
+For a cylinder aligned along the $z$-axis:
\beq
d_g(\ve{r}_i;\ve{R}_i) = \sqrt{ (x_i-X_i)^2 + (y_i - Y_i)^2 }
\eeq
\subsubsection{Constraints}
\label{subsubsec:constraints}
-\newcommand{\clam}{C_{\lambda}}
The constraints are formally part of the Hamiltonian, and therefore
they give a contribution to the free energy. In {\gromacs} this can be
calculated using the \normindex{LINCS} or the \normindex{SHAKE} algorithm.
-If we have a number of constraint equations $g_k$:
+If we have $k = 1 \ldots K$ constraint equations $g_k$ for LINCS, then
\beq
-g_k = \ve{r}_{k} - d_{k}
+g_k = |\ve{r}_{k}| - d_{k}
\eeq
-where $\ve{r}_k$ is the distance vector between two particles and
-$d_k$ is the constraint distance between the two particles, we can write
-this using a $\LAM$-dependent distance as
+where $\ve{r}_k$ is the displacement vector between two particles and
+$d_k$ is the constraint distance between the two particles. We can express
+the fact that the constraint distance has a $\LAM$ dependency by
\beq
-g_k = \ve{r}_{k} - \left(\LL d_{k}^A + \LAM d_k^B\right)
+d_k = \LL d_{k}^A + \LAM d_k^B
\eeq
-the contribution $\clam$
-to the Hamiltonian using Lagrange multipliers $\lambda$:
+
+Thus the $\LAM$-dependent constraint equation is
+\beq
+g_k = |\ve{r}_{k}| - \left(\LL d_{k}^A + \LAM d_k^B\right).
+\eeq
+
+The (zero) contribution $G$ to the Hamiltonian from the constraints
+(using Lagrange multipliers $\lambda_k$, which are logically distinct
+from the free-energy $\LAM$) is
\bea
-\clam &=& \sum_k \lambda_k g_k \\
-\dvdl{\clam} &=& \sum_k \lambda_k \left(d_k^B-d_k^A\right)
+G &=& \sum^K_k \lambda_k g_k \\
+\dvdl{G} &=& \frac{\partial G}{\partial d_k} \dvdl{d_k} \\
+ &=& - \sum^K_k \lambda_k \left(d_k^B-d_k^A\right)
\eea
+For SHAKE, the constraint equations are
+\beq
+g_k = \ve{r}_{k}^2 - d_{k}^2
+\eeq
+with $d_k$ as before, so
+\bea
+\dvdl{G} &=& -2 \sum^K_k \lambda_k \left(d_k^B-d_k^A\right)
+\eea
\subsection{Soft-core interactions\index{soft-core interactions}}
\begin{figure}
For both Coulomb and van der Waals interactions there are interaction
type selectors (termed {\tt vdwtype} and {\tt coulombtype}) and two
parameters, for a total of six non-bonded interaction parameters. See
-\secref{mdpopt} for a complete description of these parameters.
+the User Guide for a complete description of these parameters.
The neighbor searching (NS) can be performed using a single-range, or a twin-range
approach. Since the former is merely a special case of the latter, we will
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