Remove IMD manual section

This should be re-attached to the code patch in due course.

Change-Id: Iad750fe3bc5f855e5a5831bf29b0c00e6cf4e6a9

diff --git a/manual/special.tex b/manual/special.tex
index ca7b9a5378a69b76d11427fac28518e11c663c4e..db543530d91f7f637ad2545eb4496e1864397dcc 100644 (file)
--- a/manual/special.tex
+++ b/manual/special.tex
@@ -1911,53 +1911,6 @@ can be used at run time to specify a path where these plug-ins can be
 found. Note that these plug-ins are in a binary format, and that format
 must match the architecture of the machine attempting to use them.
 
-\section{Interactive Molecular Dynamics}
-{\gromacs} supports the Interactive molecular dynamics (IMD) protocol as implemented by VMD to
-control a running simulation in NAMD.  IMD allows monitoring of running simulation from a VMD client.
-In addition, the user can interact with the simulation by pulling on atoms, residues or fragments with a
-mouse or force-feedback devices.
-
-\subsection{Simulation input preparation}
-The {\gromacs} implementation allows transmission and interaction with a part of the running simulation
-only, e.g. in cases where no water molecules should be transmitted or pulled. The group is specified
-via the {\tt IMD-group} {\tt .mdp} option. When {\tt IMD-group} is empty, the IMD protocol
-is disabled and cannot be enabled via the switches in {\tt mdrun}. To interact with the entire
-system, {\tt IMD-group} has to be set to {\tt System}, which is also the default for {\tt .tpr}
-files created with an older version without IMD implementation. When using {\tt grompp}, a {\tt .gro} file
-to be used with VMD is written out ({\tt -imd} switch of {\tt grompp}).
-
-\subsection{Starting the simulation}
-Communication between VMD and {\gromacs} is achieved via tcp-sockets and thus enables controlling
-an {\tt mdrun} running locally or on a remote cluster. The port for the connection can be
-specified with the {\tt -imdport} switch of {\tt mdrun}, 8888 is the default.
-
-Every $N$ steps, the client receives the applied forces from the VMD client and sends the new coordinates to the client.
-The initial frequency for communication with the client is set to the global communication frequency but can
-be altered using the {\tt -imdfreq} switch. VMD also permits increasing or decreasing the communication
-frequency interactively.
-
-By default, the simulation starts and runs even if no IMD client is connected. This behavior is changed by the
-{\tt -imdwait} switch of {\tt mdrun}. After startup and whenever the client has disconnected, the integration
-stops until reconnection of the client.
-
-When the {\tt -imdterm} switch is used, the simulation can be terminated pressing the stop button in VMD. This is disabled by
-default.
-
-Finally, to turn on interaction with the simulation (i.e. pulling from VMD) the {\tt -imdpull} switch has to be used.
-
-Therefore, a simulation can only be monitored but not influenced from the VMD client when none of {\tt -imdwait},
-{\tt -imdterm} or {\tt -imdpull} are set. However, since the IMD protocol requires no authentication, it is not
-advisable to run simulations on a host directly reachable from an insecure environment. Secure shell forwarding of {\tt TCP}
-can be used to connect to running simulations not directly reachable from the interacting host.
-
-\subsection{Connecting from VMD}
-In VMD, first the structure corresponding to the IMD group has to be loaded (File $\rightarrow$ New Molecule\ldots). Then
-the IMD connection window has to be used (Extensions $\rightarrow$ Simulation $\rightarrow$ IMD Connect (NAMD)). In the IMD connection
-window, hostname and port have to be specified and followed by pressing Connect. Detach Sim allows disconnecting without
-terminating the simulation, while Stop Sim ends the simulation on the next neighbor searching step (if allowed by {\tt -imdterm}).
-
-The timestep transfer rate allows adjusting the communication frequency between simulation and IMD client. Setting the keep rate loads every $N^\mathrm{th}$ frame into VMD instead of discarding them when a new one is received. The displayed energies are in SI units in contrast to energies displayed from NAMD simulations.
-
 
 % LocalWords:  PMF pmf kJ mol Jarzynski BT bilayer rup mdp AFM fepmf fecalc rb
 % LocalWords:  posre grompp fs Verlet dihedrals hydrogens hydroxyl sulfhydryl