Added pull geometry direction-relative

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

diff --git a/docs/manual/special.tex b/docs/manual/special.tex
index d79a680e5816d99e2c2cfbf660d0985fd6ed35e0..045f5a4dbcf7e208e2dd07a095e79b388696000d 100644 (file)
--- a/docs/manual/special.tex
+++ b/docs/manual/special.tex
@@ -180,7 +180,7 @@ a canonical ensemble of the initial state A and $\beta=1/k_B T$.
 The pull code applies forces or constraints between the centers
 of mass of one or more pairs of groups of atoms.
 Each pull reaction coordinate is called a ``coordinate'' and it operates
-on two pull groups. A pull group can be part of one or more pull
+on usually two, but sometimes more, pull groups. A pull group can be part of one or more pull
 coordinates. Furthermore, a coordinate can also operate on a single group
 and an absolute reference position in space.
 The distance between a pair of groups can be determined
@@ -194,7 +194,7 @@ weighting factor can also be used.
 with umbrella pulling. $V_{rup}$ is the velocity at which the spring is
 retracted, $Z_{link}$ is the atom to which the spring is attached and
 $Z_{spring}$ is the location of the spring.}
-\label{fi:pull} 
+\label{fig:pull} 
 \end{figure}
 
 Three different types of calculation are supported,
@@ -264,7 +264,7 @@ of 0.79 times the radius.
 reference group applied to interface systems. C is the reference group.
 The circles represent the center of mass of two groups plus the reference group,
 $d_c$ is the reference distance.}
-\label{fi:pullref} 
+\label{fig:pullref} 
 \end{figure}   
 
 For a group of molecules in a periodic system, a plain reference group
@@ -306,6 +306,23 @@ as follows:
 \ve{F}_{\!i} = \frac{w'_i \, m_i}{M} \, \ve{F}_{\!com}
 \eeq
 
+\subsubsection{Definition of the pull direction}
+
+The most common setup is to pull along the direction of the vector containing
+the two pull groups, this is selected with
+{\tt pull-coord?-geometry = distance}. You might want to pull along a certain
+vector instead, which is selected with {\tt pull-coord?-geometry = direction}.
+But this can cause unwanted torque forces in the system, unless you pull against a reference group with (nearly) fixed orientation, e.g. a membrane protein embedded in a membrane along x/y while pulling along z. If your reference group does not have a fixed orientation, you should probably use
+{\tt pull-coord?-geometry = direction-relative}, see \figref{pulldirrel}.
+Since the potential now depends on the coordinates of two additional groups defining the orientation, the torque forces will work on these two groups.
+
+\begin{figure}
+\centerline{\includegraphics[width=5cm]{plots/pulldirrel}}
+\caption{The pull setup for geometry {\tt direction-relative}. The ``normal'' pull groups are 1 and 2. Groups 3 and 4 define the pull direction and thus the direction of the normal pull forces (red). This leads to reaction forces (blue) on groups 3 and 4, which are perpendicular to the pull direction. Their magnitude is given by the ``normal'' pull force times the ratio of $d_p$ and the distance between groups 3 and 4.}
+\label{fig:pulldirrel} 
+\end{figure}   
+
+
 \subsubsection{Limitations}
 There is one theoretical limitation:
 strictly speaking, constraint forces can only be calculated between