Merge branch release-2016

[alexxy/gromacs.git] / docs / manual / special.tex

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@@ -1048,6 +1048,58 @@ rotation, torques $\ve{\tau}_{\!n}$ are calculated for each slab using the
 local rotation axis of the slab and the Gaussian-weighted positions.
 
 
+\section{\normindex{Electric fields}}
+A pulsed and oscillating electric field can be applied according to:
+\begin{equation}
+E(t) = E_0 \exp\left[-\frac{(t-t_0)^2}{2\sigma^2}\right]\cos\left[\omega (t-t_0)\right]
+\label{eq_efield}
+\end{equation}
+where $E_0$ is the field strength, the angular frequency \mbox{$\omega = 2\pi c/\lambda$}, $t_0$ is
+the time at of the peak in the field strength and $\sigma$ is the with
+of the pulse. Special cases occur when $\sigma$ = 0 (non-pulsed field)
+and for $\omega$ is 0 (static field).
+
+This simulated \normindex{laser}-pulse was applied to
+simulations of melting ice~\cite{Caleman2008a}. A pulsed electric field may
+look ike Fig.~\ref{fig:field}. In the supporting
+information of that paper the impact of an applied electric field on a
+system under periodic boundary conditions is analyzed. It is described
+that the effective electric field under PBC is larger than the applied
+field, by a factor depending on the size of the box and the dielectric
+properties of molecules in the box. For a system with static dielectric
+properties this factor can be corrected for. But for a system where
+the dielectric varies over time, for example a membrane protein with
+a pore that opens and closes during the simulatippn, this way of applying
+an electric field is not useful. In such cases one can use the computational
+electrophysiology protocol described in the next section (\secref{compel}).
+\begin{figure}[ht]
+\centerline{\includegraphics[width=8cm]{plots/field}}
+\caption {A simulated laser pulse in GROMACS.}
+\label{fig:field}
+\end{figure}
+
+Electric fields are applied when the following options are specified
+in the {\tt grompp.mdp} file. You specify, in order, $E_0$, $\omega$,
+$t_0$ and $\sigma$:
+\begin{verbatim}
+ElectricField-x = 0.04 0       0     0
+\end{verbatim}
+yields a static field with $E_0$ = 0.04 V/nm in the X-direction. In contrast,
+\begin{verbatim}
+ElectricField-x = 2.0  150     5     0
+\end{verbatim}
+yields an oscillating electric field with $E_0$ = 2 V/nm, $\omega$ = 150/ps and
+$t_0$ = 5 ps. Finally 
+\begin{verbatim}
+ElectricField-x = 2.0  150     5     1
+\end{verbatim}
+yields an pulsed-oscillating electric field with $E_0$ = 2 V/nm, $\omega$ = 150/ps and
+$t_0$ = 5 ps and $\sigma$ = 1 ps. Read more in ref.~\cite{Caleman2008a}.
+Note that the input file format is changed from the undocumented older
+version. A figure like Fig.~\ref{fig:field} may be produced by passing
+the {\tt -field} option to {\tt gmx mdrun}.
+
+
 \section{\normindex{Computational Electrophysiology}}
 \label{sec:compel}