- Reference tools as 'gmx <tool>' instead of the old names.
- Expand the section on selections now that there actually are some
tools that can use the full power.
- Rewrite sections that were referencing obsolete tools (g_bond and
g_sgangle).
- Remove references to tools that aren't there.
Change-Id: Iee99f69e2d4effa585d98930ef1d78c1367e2ec0
%
% This file is part of the GROMACS molecular simulation package.
%
-% Copyright (c) 2013, by the GROMACS development team, led by
+% Copyright (c) 2013,2014, 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.
The output files are often produced as finished Grace/Xmgr graphs.
First, in \secref{usinggroups}, the group concept in analysis is explained.
+\ssecref{selections} explains a newer concept of dynamic selections,
+which is currently supported by a few tools.
Then, the different analysis tools are presented.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Groups in Analysis
\section{Using Groups}
\label{sec:usinggroups}\index{groups}
-{\tt make_ndx, mk_angndx}\\
+{\tt gmx make_ndx, gmx mk_angndx, gmx select}\\
In \chref{algorithms}, it was explained how {\em groups of
-atoms} can be used in {\tt mdrun} (see~\secref{groupconcept}). In most analysis programs, groups
+atoms} can be used in {\tt mdrun} (see~\secref{groupconcept}).
+In most analysis programs, groups
of atoms must also be chosen. Most programs can generate several default
index groups, but groups can always be read from an index file. Let's
consider the example of a simulation of a binary mixture of components A and B. When
index.ndx}), there are a couple of programs to generate them, using
either your input configuration or the topology. To generate an
index file consisting of a series of {\em atom numbers} (as in the
-example of $g_{AB}$), use {\tt \normindex{make_ndx}} or
-{\tt \normindex{g_select}}. To generate an index file
-with angles or dihedrals, use {\tt \normindex{mk_angndx}}. Of course you can also
+example of $g_{AB}$), use {\tt \normindex{gmx make_ndx}} or
+{\tt \normindex{gmx select}}. To generate an index file
+with angles or dihedrals, use {\tt \normindex{gmx mk_angndx}}.
+Of course you can also
make them by hand. The general format is presented here:
\begin{verbatim}
\subsection{Selections}
\label{subsec:selections}
-{\tt \normindex{g_select}}\\
-{\gromacs} also includes a {\tt g_select} tool that can be used to
-select atoms based on more flexible criteria than in {\tt make_ndx},
-including selecting atoms based on their coordinates. Currently, the
-tool is experimental and only supports some basic operations, but in the
-future the functionality is planned to be included in other analysis
-tools as well. A description of possible ways to select atoms can be
-read by running {\tt g_select} and typing {\tt help} at the selection
-prompt that appears. It is also possible to write your own analysis
+{\tt \normindex{gmx select}}\\
+Currently, a few analysis tools support an extended concept of {\em
+(dynamic) \normindex{selections}}. There are three main differences to
+traditional index groups:
+\begin{itemize}
+ \item The selections are specified as text instead of reading fixed
+ atom indices from a file, using a syntax similar to VMD. The text
+ can be entered interactively, provided on the command line, or from
+ a file.
+ \item The selections are not restricted to atoms, but can also specify
+ that the analysis is to be performed on, e.g., center-of-mass
+ positions of a group of atoms.
+ Some tools may not support selections that do not evaluate to single
+ atoms, e.g., if they require information that is available only for
+ single atoms, like atom names or types.
+ \item The selections can be dynamic, i.e., evaluate to different atoms
+ for different trajectory frames. This allows analyzing only a
+ subset of the system that satisfies some geometric criteria.
+\end{itemize}
+As an example of a simple selection,
+{\tt resname ABC and within 2 of resname DEF}
+selects all atoms in residues named ABC that are within 2\,nm of any
+atom in a residue named DEF.
+
+Tools that accept selections can also use traditional index files
+similarly to older tools: it is possible to give an {\tt .ndx} file to
+the tool, and directly select a group from the index file as a
+selection, either by group number or by group name. The index groups
+can also be used as a part of a more complicated selection.
+
+To get started, you can run {\tt gmx select} with a single structure,
+and use the interactive prompt to try out different selections.
+The tool provides, among others, output options {\tt -on} and
+{\tt -ofpdb} to write out the selected atoms to an index file and to a
+{\tt .pdb} file, respectively. This does not allow testing selections
+that evaluate to center-of-mass positions, but other selections can be
+tested and the result examined.
+
+The detailed syntax and the individual keywords that can be used in
+selections can be accessed by typing {\tt help} in the interactive
+prompt of any selection-enabled tool, as well as with
+{\tt gmx help selections}. The help is divided into subtopics that can
+be accessed with, e.g., {\tt help syntax} / {\tt gmx help selections
+syntax}. Some individual selection keywords have extended help as well,
+which can be accessed with, e.g., {\tt help keywords within}.
+
+The interactive prompt does not currently provide much editing
+capabilities. If you need them, you can run the program under
+{\tt rlwrap}.
+
+For tools that do not yet support the selection syntax, you can use
+{\tt gmx select -on} to generate static index groups to pass to the
+tool. However, this only allows for a small subset (only the first
+bullet from the above list) of the flexibility that fully
+selection-aware tools offer.
+
+It is also possible to write your own analysis
tools to take advantage of the flexibility of these selections: see the
-{\tt template.c} file in the {\tt share/gromacs/template} directory of
+{\tt template.cpp} file in the {\tt share/gromacs/template} directory of
your installation for an example.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Looking at your trajectory
\section{Looking at your trajectory}
\label{sec:lookwhostalking}
-{\tt ngmx}\\
\begin{figure}
\centerline{
{\includegraphics[width=8cm,angle=90]{plots/ngmxdump}}}
-\caption{The window of {\tt ngmx} showing a box of water.}
+\caption{The window of {\tt gmx view} showing a box of water.}
\label{fig:ngmxdump}
\end{figure}
-
+{\tt gmx view}\\
Before analyzing your trajectory it is often informative to look at
your trajectory first. {\gromacs} comes with a simple trajectory
-viewer {\tt \normindex{ngmx}}; the advantage with this one is that it does not
+viewer {\tt \normindex{gmx view}}; the advantage with this one is that it does not
require OpenGL, which usually isn't present on {\eg} supercomputers.
It is also possible to generate a
hard-copy in Encapsulated Postscript format (see
\section{General properties}
\label{sec:genprop}
-{\tt g_energy, g_traj}\\
+{\tt gmx energy, gmx traj}\\
To analyze some or all {\em energies} and other properties, such as
{\em total pressure}, {\em pressure tensor}, {\em density}, {\em
-box-volume} and {\em box-sizes}, use the program {\tt \normindex{g_energy}}. A
+box-volume} and {\em box-sizes}, use the program {\tt \normindex{gmx energy}}. A
choice can be made from a list a set of energies, like potential,
kinetic or total energy, or individual contributions, like
Lennard-Jones or dihedral energies.
{\bf v}_{com} = {1 \over M} \sum_{i=1}^N m_i {\bf v}_i
\eeq
with $M = \sum_{i=1}^N m_i$ the total mass of the system, can be
-monitored in time by the program {\tt \normindex{g_traj} -com -ov}. It is however
+monitored in time by the program {\tt \normindex{gmx traj} -com -ov}. It is however
recommended to remove the center-of-mass velocity every step (see
\chref{algorithms})!
\section{Radial distribution functions}
\label{sec:rdf}
-{\tt g_rdf}\\
+{\tt gmx rdf}\\
The {\em radial distribution function} (RDF) or pair correlation
function $g_{AB}(r)$ between particles of type $A$ and $B$ is defined
in the following way:
\begin{figure}
\centerline{
{\includegraphics[width=7cm,angle=270]{plots/rdf}}}
-\caption[Definition of slices in {\tt g_rdf}.]{Definition of slices
-in {\tt g_rdf}: A. $g_{AB}(r)$. B. $g_{AB}(r,\theta)$. The slices are
+\caption[Definition of slices in {\tt gmx rdf}.]{Definition of slices
+in {\tt gmx rdf}: A. $g_{AB}(r)$. B. $g_{AB}(r,\theta)$. The slices are
colored gray. C. Normalization $\langle\rho_B\rangle_{local}$. D. Normalization
$\langle\rho_B\rangle_{local,\:\theta }$. Normalization volumes are colored gray.}
\label{fig:rdfex}
Usually the value of $r_{max}$ is half of the box length. The
averaging is also performed in time. In practice the analysis program
-{\tt \normindex{g_rdf}} divides the system into spherical slices (from $r$ to
+{\tt \normindex{gmx rdf}} divides the system into spherical slices (from $r$ to
$r+dr$, see \figref{rdfex}A) and makes a histogram in stead of
the $\delta$-function. An example of the RDF of oxygen-oxygen in
SPC water~\cite{Berendsen81} is given in \figref{rdf}.
\label{fig:rdf}
\end{figure}
-With {\tt g_rdf} it is also possible to calculate an angle dependent rdf
+% TODO: This functionality isn't there...
+With {\tt gmx rdf} it is also possible to calculate an angle dependent rdf
$g_{AB}(r,\theta)$, where the angle $\theta$ is defined with respect to a
certain laboratory axis ${\bf e}$, see \figref{rdfex}B.
\bea
can actually be obtained experimentally using {\eg} NMR or other relaxation
experiments. {\gromacs} can compute correlations using
the 1$^{st}$ and 2$^{nd}$ order Legendre polynomial (\eqnref{corrleg}).
-This can also be used for rotational autocorrelation ({\tt \normindex{g_rotacf}})
-and dipole autocorrelation ({\tt \normindex{g_dipoles}}).
+This can also be used for rotational autocorrelation
+({\tt \normindex{gmx rotacf}})
+and dipole autocorrelation ({\tt \normindex{gmx dipoles}}).
In order to study torsion angle dynamics, we define a dihedral
autocorrelation function as~\cite{Spoel97a}:
\eeq
\subsection{Some Applications}
-The program {\tt \normindex{g_velacc}} calculates the {\em velocity autocorrelation
+The program {\tt \normindex{gmx velacc}} calculates the {\em velocity autocorrelation
function}.
\beq
C_{\ve{v}} (\tau) ~=~ \langle {\ve{v}}_i(\tau) \cdot {\ve{v}}_i(0) \rangle_{i \in A}
Another important quantity is the dipole correlation time. The {\em dipole
correlation function} for particles of type $A$ is calculated as follows by
-{\tt \normindex{g_dipoles}}:
+{\tt \normindex{gmx dipoles}}:
\beq
C_{\mu} (\tau) ~=~
\langle {\bf \mu}_i(\tau) \cdot {\bf \mu}_i(0) \rangle_{i \in A}
The \normindex{viscosity} of a liquid can be related to the correlation
time of the Pressure tensor $\ve{P}$~\cite{PSmith93c,Balasubramanian96}.
-{\tt \normindex{g_energy}} can compute the viscosity,
+{\tt \normindex{gmx energy}} can compute the viscosity,
but this is not very accurate~\cite{Hess2002a}, and
actually the values do not converge.
%} % Brace matches ifthenelse test for gmxlite
\section{Mean Square Displacement}
\label{sec:msd}
-{\tt g_msd}\\
+{\tt gmx msd}\\
To determine the self \index{diffusion coefficient} $D_A$ of
particles of type $A$, one can use the \normindex{Einstein
relation}~\cite{Allen87}:
\|{\bf r}_i(t) - {\bf r}_i(0)\|^2 \rangle_{i \in A} ~=~ 6 D_A t
\eeq
This {\em mean square displacement} and $D_A$ are calculated by the
-program {\tt \normindex{g_msd}}. Normally an index file containing
+program {\tt \normindex{gmx msd}}. Normally an index file containing
atom numbers is used and the MSD is averaged over these atoms. For
molecules consisting of more than one atom, ${\bf r}_i$ can be taken
as the center of mass positions of the molecules. In that case, you
should use an index file with molecule numbers. The results will be
-nearly identical to averaging over atoms, however. The {\tt g_msd}
+nearly identical to averaging over atoms, however. The {\tt gmx msd}
program can
also be used for calculating diffusion in one or two dimensions. This
is useful for studying lateral diffusion on interfaces.
%
%%%%%%%%%%%%%%%%%%%%% Bonds, angles and dihedral %%%%%%%%%%%%%%%%%%%
%
-\section{Bonds, angles and dihedrals}
+\section{Bonds/distances, angles and dihedrals}
\label{sec:bad}
-{\tt g_bond, g_angle, g_sgangle}\\
-To monitor specific {\em bonds} in your molecules during time, the program
-{\tt \normindex{g_bond}} calculates the distribution of the bond length in time.
-The index file consists of pairs of atom numbers, for example\\
-
+{\tt gmx distance, gmx angle, gmx gangle}\\
+To monitor specific {\em bonds} in your modules, or more generally
+distances between points, the program
+{\tt \normindex{gmx distance}} can calculate distances as a function of
+time, as well as the distribution of the distance.
+With a traditional index file, the groups should consist of pairs of
+atom numbers, for example:
\begin{verbatim}
[ bonds_1 ]
1 2
[ bonds_2 ]
12 13
\end{verbatim}
+Selections are also supported, with first two positions defining the
+first distance, second pair of positions defining the second distance
+and so on. You can calculate the distances between CA and CB atoms in
+all your residues (assuming that every residue either has both atoms, or
+neither) using a selection such as:
+\begin{verbatim}
+name CA CB
+\end{verbatim}
+The selections also allow more generic distances to be computed.
+For example, to compute the distances between centers of mass of two
+residues, you can use:
+\begin{verbatim}
+com of resname AAA plus com of resname BBB
+\end{verbatim}
-The program {\tt \normindex{g_angle}} calculates the distribution of {\em angles} and
+The program {\tt \normindex{gmx angle}} calculates the distribution of {\em angles} and
{\em dihedrals} in time. It also gives the average angle or dihedral.
The index file consists of triplets or quadruples of atom numbers:
\label{fig:dih_def}
\end{figure}
-To follow specific {\em angles} in time between two vectors, a vector
-and a plane or two planes (defined by 2 or 3 atoms, respectively, inside your
-molecule, see \figref{sgangle}A, B, C), use the program {\tt \normindex{g_sgangle}}.
+The program {\tt \normindex{gmx gangle}} provides a selection-enabled
+version to compute angles. This tool can also compute angles and
+dihedrals, but does not support all the options of {\tt gmx angle}, such
+as autocorrelation or other time series analyses.
+In addition, it supports angles between two vectors, a vector and a
+plane, two planes (defined by 2 or 3 points, respectively), a
+vector/plane and the $z$ axis, or a vector/plane and the normal of a
+sphere (determined by a single position).
+Also the angle between a vector/plane compared to its position in the
+first frame is supported.
+For planes, {\tt \normindex{gmx gangle}} uses the normal vector
+perpendicular to the plane.
+See \figref{sgangle}A, B, C) for the definitions.
\begin{figure}
\centerline{
-{\includegraphics[width=6.5cm,angle=270]{plots/sgangle}}}
-\caption[Options of {\tt g_sgangle}.]{Options of {\tt g_sgangle}: A. Angle between 2 vectors. B. Angle between a vector and the normal of a plane. C. Angle between two planes. D. Distance between the geometrical centers of 2 planes. E. Distances between a vector and the center of a plane.}
+{\includegraphics{plots/sgangle}}}
+\caption[Angle options of {\tt gmx gangle}.]{Angle options of {\tt gmx gangle}:
+A. Angle between two vectors.
+B. Angle between two planes.
+C. Angle between a vector and the $z$ axis.
+D. Angle between a vector and the normal of a sphere.
+Also other combinations are supported: planes and vectors can be used
+interchangeably.}
\label{fig:sgangle}
\end{figure}
-
-For planes, {\tt \normindex{g_sgangle}} uses the normal vector perpendicular to the plane. It
-can also calculate the {\em distance} $d$ between the geometrical
-center of two planes (see \figref{sgangle}D), and the distances
-$d_1$ and $d_2$ between 2 atoms (of a vector) and the center of a
-plane defined by 3 atoms (see \figref{sgangle}D). It further
-calculates the distance $d$ between the center of the plane and the
-middle of this vector. Depending on the input groups ({\ie} groups of
-2 or 3 atom numbers), the program decides what angles and distances to
-calculate. For example, the index-file could look like this:
-
-\begin{verbatim}
-[ a_plane ]
- 1 2 3
-
-[ a_vector ]
- 4 5
-\end{verbatim}
%} % Brace matches ifthenelse test for gmxlite
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Radius of gyration and distances
\section{Radius of gyration and distances}
\label{sec:rg}
-{\tt g_gyrate, g_sgangle, g_mindist, g_mdmat, xpm2ps}\\
+{\tt gmx gyrate, gmx distance, gmx mindist, gmx mdmat, gmx xpm2ps}\\
To have a rough measure for the compactness of a structure, you can calculate
-the {\em radius of gyration} with the program {\tt \normindex{g_gyrate}} as follows:
+the {\em radius of gyration} with the program {\tt \normindex{gmx gyrate}} as follows:
\beq
R_g ~=~ \left({\frac{\sum_i \|{\bf r}_i\|^2 m_i}{\sum_i m_i}}\right)^{\half}
\label{eqn:rg}
The {\em distance between the geometrical centers} of two groups can be
calculated with the program
%\ifthenelse{\equal{\gmxlite}{1}}{
-%{\tt \normindex{g_sgangle}}.}
-{{\tt \normindex{g_sgangle}}, as explained in \secref{bad}.}
+{{\tt \normindex{gmx distance}}, as explained in \secref{bad}.}
\item[$\bullet$]
The {\em minimum distance} between two groups of atoms during time
-can be calculated with the program {\tt \normindex{g_mindist}}. It also calculates the
+can be calculated with the program {\tt \normindex{gmx mindist}}. It also calculates the
{\em number of contacts} between these groups
within a certain radius $r_{max}$.
\item[$\bullet$]
To monitor the {\em minimum distances between amino acid residues}
within a (protein) molecule, you can use
-the program {\tt \normindex{g_mdmat}}. This minimum distance between two residues
+the program {\tt \normindex{gmx mdmat}}. This minimum distance between two residues
A$_i$ and A$_j$ is defined as the smallest distance between any pair of
atoms (i $\in$ A$_i$, j $\in$ A$_j$).
The output is a symmetrical matrix of smallest distances
\section{Root mean square deviations in structure}
\label{sec:rmsd}
-{\tt g_rms, g_rmsdist}\\
+{\tt gmx rms, gmx rmsdist}\\
The {\em root mean square deviation} ($RMSD$) of certain atoms in a molecule
with respect to a reference structure can be calculated with the program
-{\tt \normindex{g_rms}} by least-square fitting the structure to the reference structure
+{\tt \normindex{gmx rms}} by least-square fitting the structure to the reference structure
($t_2 = 0$) and subsequently calculating the $RMSD$ (\eqnref{rmsd}).
\beq
RMSD(t_1,t_2) ~=~ \left[\frac{1}{M} \sum_{i=1}^N m_i \|{\bf r}_i(t_1)-{\bf r}_i(t_2)\|^2 \right]^{\frac{1}{2}}
such a matrix.
Alternatively the $RMSD$ can be computed using a fit-free method with the
-program {\tt \normindex{g_rmsdist}}:
+program {\tt \normindex{gmx rmsdist}}:
\beq
RMSD(t) ~=~ \left[\frac{1}{N^2}\sum_{i=1}^N \sum_{j=1}^N \|{\bf r}_{ij}(t)-{\bf r}_{ij}(0)\|^2\right]^{\frac{1}{2}}
\label{eqn:rmsdff}
the potential, but with random diffusion.
The covariance matrix is built and diagonalized by
-{\tt \normindex{g_covar}}.
+{\tt \normindex{gmx covar}}.
The principal components and overlap (and many more things)
-can be plotted and analyzed with {\tt \normindex{g_anaeig}}.
-The cosine content can be calculated with {\tt \normindex{g_analyze}}.
+can be plotted and analyzed with {\tt \normindex{gmx anaeig}}.
+The cosine content can be calculated with {\tt \normindex{gmx analyze}}.
%} % Brace matches ifthenelse test for gmxlite
%\ifthenelse{\equal{\gmxlite}{1}}{}{
\section{Dihedral principal component analysis}
-{\tt g_angle, g_covar, g_anaeig}\\
+{\tt gmx angle, gmx covar, gmx anaeig}\\
Principal component analysis can be performed in dihedral
space~\cite{Mu2005a} using {\gromacs}. You start by defining the
dihedral angles of interest in an index file, either using {\tt
- mk_angndx} or otherwise. Then you use the {\tt g_angle} program
+ gmx mk_angndx} or otherwise. Then you use the {\tt gmx angle} program
with the {\tt -or} flag to produce a new {\tt .trr} file containing the cosine and
sine of each dihedral angle in two coordinates, respectively. That is,
in the {\tt .trr} file you will have a series of numbers corresponding to:
cos($\phi_1$), sin($\phi_1$), cos($\phi_2$), sin($\phi_2$), ...,
cos($\phi_n$), sin($\phi_n$), and the array is padded with zeros, if
necessary. Then you can use this {\tt .trr} file as input for the {\tt
- g_covar} program and perform principal component analysis as usual.
+ gmx covar} program and perform principal component analysis as usual.
For this to work you will need to generate a reference file ({\tt .tpr},
{\tt .gro}, {\tt .pdb} etc.) containing the same number of ``atoms''
as the new {\tt .trr} file, that is for $n$ dihedrals you need 2$n$/3 atoms
(rounded up if not an integer number).
You should use the {\tt -nofit} option for {\tt
- g_covar} since the coordinates in the dummy reference file do not
+gmx covar} since the coordinates in the dummy reference file do not
correspond in any way to the information in the {\tt .trr} file. Analysis of
-the results is done using {\tt g_anaeig}.
+the results is done using {\tt gmx anaeig}.
%} % Brace matches ifthenelse test for gmxlite
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Hydrogen bonds
\section{Hydrogen bonds}
-{\tt g_hbond}\\
-The program {\tt \normindex{g_hbond}} analyzes the {\em hydrogen bonds} (H-bonds)
+{\tt gmx hbond}\\
+The program {\tt \normindex{gmx hbond}} analyzes the {\em hydrogen bonds} (H-bonds)
between all possible donors D and acceptors A. To determine if an
H-bond exists, a geometrical criterion is used, see also
\figref{hbond}:
The value of $r_{HB} = 0.35$~nm corresponds to the first minimum of the RDF of
SPC water (see also \figref{rdf}).
-The program {\tt g_hbond} analyzes all hydrogen bonds existing
+The program {\tt gmx hbond} analyzes all hydrogen bonds existing
between two groups of atoms (which must be either identical or
non-overlapping) or in specified donor-hydrogen-acceptor triplets, in
the following ways:
donor-hydrogen-acceptor triplets involved in hydrogen bonds between
the analyzed groups and all solvent atoms involved in insertion.
-% The {\tt -ins} option appears to have been removed during the course of version 4.5 development
-% \item
-% Solvent insertion into H-bonds can be analyzed, see
-% \figref{insert}. In this case an additional group identifying
-% the solvent must be selected. The occurrence of insertion will be
-% indicated in the existence map. {\bf Note} that insertion into and existence
-% of a specific H-bond can occur simultaneously and will also be
-% indicated as such in the existence map.
-
\end{itemize}
%\ifthenelse{\equal{\gmxlite}{1}}{}{
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Protein related items
\section{Protein-related items}
-{\tt do_dssp, g_rama, g_xrama, g_wheel}\\
+{\tt gmx do_dssp, gmx rama, gmx wheel}\\
To analyze structural changes of a protein, you can calculate the radius of
gyration or the minimum residue distances over time
(see \secref{rg}), or calculate the RMSD (\secref{rmsd}).
You can also look at the changing of {\em secondary structure elements}
-during your run. For this, you can use the program {\tt \normindex{do_dssp}}, which is
+during your run. For this, you can use the program {\tt \normindex{gmx do_dssp}}, which is
an interface for the commercial program {\tt DSSP}~\cite{Kabsch83}. For
further information, see the {\tt DSSP} manual. A typical output plot of
-{\tt do_dssp} is given in \figref{dssp}.
+{\tt gmx do_dssp} is given in \figref{dssp}.
\begin{figure}
\centerline{
\label{fig:phipsi}
\end{figure}
-To evaluate this Ramachandran plot you can use the program {\tt \normindex{g_rama}}.
+To evaluate this Ramachandran plot you can use the program {\tt
+\normindex{gmx rama}}.
A typical output is given in \figref{rama}.
\begin{figure}
\label{fig:rama}
\end{figure}
-It is also possible to generate an animation of the Ramachandran plot
-in time. This can be useful for analyzing certain dihedral transitions
-in your protein. You can use the program {\tt \normindex{g_xrama}} for this.
-
When studying $\alpha$-helices
it is useful to have a {\em helical wheel} projection
of your peptide, to see whether a peptide is amphipathic. This can be done
-using the {\tt \normindex{g_wheel}} program. Two examples are
+using the {\tt \normindex{gmx wheel}} program. Two examples are
plotted in \figref{wheel}.
\begin{figure}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Membrane Related Items
\section{Interface-related items}
-{\tt g_order, g_density, g_potential, g_traj}\\
+{\tt gmx order, gmx density, gmx potential, gmx traj}\\
When simulating molecules with long carbon tails, it can be
interesting to calculate their average orientation. There are several
flavors of order parameters, most of which are related. The program
-{\tt \normindex{g_order}} can calculate order parameters using the equation:
+{\tt \normindex{gmx order}} can calculate order parameters using the equation:
\begin{equation}
S_{z} = \frac{3}{2}\langle {\cos^2{\theta_z}} \rangle - \frac{1}{2}
where the position $z=-\infty$ is far enough in the bulk phase such that
the field is zero. With this method, it is possible to ``split'' the
total potential into separate contributions from lipid and water
-molecules. The program {\tt \normindex{g_potential}} divides the box in slices and
+molecules. The program {\tt \normindex{gmx potential}} divides the box in slices and
sums all charges of the atoms in each slice. It then integrates this
charge density to give the electric field, which is in turn integrated to
give the potential. Charge density, electric field, and potential are written
to {\tt xvgr} input files.
-The program {\tt \normindex{g_traj}} is a very simple analysis program. All it
+The program {\tt \normindex{gmx traj}} is a very simple analysis program. All it
does is print the coordinates, velocities, or forces of selected atoms.
It can also calculate the center of mass of one or more
molecules and print the coordinates of the center of mass to three
having the coordinates of selected molecules or atoms can be very
handy for further analysis, not only in interfacial systems.
-%
-% Non-existent program
-% The program {\tt \normindex{g_pvd}} calculates a lot of properties, among which
-% the density of a group in particles per unit of volume, but not a
-% density that takes the mass of the atoms into account. The program
-%
-
-The program {\tt \normindex{g_density}} also calculates the density of groups,
-but takes the masses into account and gives a plot of the density against a box
+The program {\tt \normindex{gmx density}} calculates the mass density of
+groups and gives a plot of the density against a box
axis. This is useful for looking at the distribution of groups or
atoms across the interface.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Chemical shifts
-\section{Chemical shifts}
-{\tt total, do_shift}\\
-You can compute the NMR chemical shifts of protons with the program
-{\tt \normindex{do_shift}}. This is just an {\gromacs} interface to
-the public domain program {\tt total}~\cite{Williamson93a}. For
-further information, read the article. Although there is limited
-support for this in {\gromacs}, users are encouraged to use the
-software provided by David Case's group at Scripps because it seems
-to be more up-to-date.
+% \section{Chemical shifts}
+% {\tt total, do_shift}\\
+% You can compute the NMR chemical shifts of protons with the program
+% {\tt \normindex{do_shift}}. This is just an {\gromacs} interface to
+% the public domain program {\tt total}~\cite{Williamson93a}. For
+% further information, read the article. Although there is limited
+% support for this in {\gromacs}, users are encouraged to use the
+% software provided by David Case's group at Scripps because it seems
+% to be more up-to-date.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%} % Brace matches ifthenelse test for gmxlite
+++ /dev/null
-%!PS-Adobe-2.0 EPSF-2.0
-%%Title: sgangle.fig
-%%Creator: fig2dev Version 3.1 Patchlevel 2
-%%CreationDate: Thu Aug 26 16:06:10 1999
-%%For: anton@rugmd23.chem.rug.nl (K.A.Feenstra,17.14,,)
-%Magnification: 0.70
-%%Orientation: Landscape
-%%BoundingBox: 0 0 390 724
-%%Pages: 0
-%%BeginSetup
-%%IncludeFeature: *PageSize Letter
-%%EndSetup
-%%EndComments
-/$F2psDict 200 dict def
-$F2psDict begin
-$F2psDict /mtrx matrix put
-/col-1 {0 setgray} bind def
-/col0 {0.000 0.000 0.000 srgb} bind def
-/col1 {0.000 0.000 1.000 srgb} bind def
-/col2 {0.000 1.000 0.000 srgb} bind def
-/col3 {0.000 1.000 1.000 srgb} bind def
-/col4 {1.000 0.000 0.000 srgb} bind def
-/col5 {1.000 0.000 1.000 srgb} bind def
-/col6 {1.000 1.000 0.000 srgb} bind def
-/col7 {1.000 1.000 1.000 srgb} bind def
-/col8 {0.000 0.000 0.560 srgb} bind def
-/col9 {0.000 0.000 0.690 srgb} bind def
-/col10 {0.000 0.000 0.820 srgb} bind def
-/col11 {0.530 0.810 1.000 srgb} bind def
-/col12 {0.000 0.560 0.000 srgb} bind def
-/col13 {0.000 0.690 0.000 srgb} bind def
-/col14 {0.000 0.820 0.000 srgb} bind def
-/col15 {0.000 0.560 0.560 srgb} bind def
-/col16 {0.000 0.690 0.690 srgb} bind def
-/col17 {0.000 0.820 0.820 srgb} bind def
-/col18 {0.560 0.000 0.000 srgb} bind def
-/col19 {0.690 0.000 0.000 srgb} bind def
-/col20 {0.820 0.000 0.000 srgb} bind def
-/col21 {0.560 0.000 0.560 srgb} bind def
-/col22 {0.690 0.000 0.690 srgb} bind def
-/col23 {0.820 0.000 0.820 srgb} bind def
-/col24 {0.500 0.190 0.000 srgb} bind def
-/col25 {0.630 0.250 0.000 srgb} bind def
-/col26 {0.750 0.380 0.000 srgb} bind def
-/col27 {1.000 0.500 0.500 srgb} bind def
-/col28 {1.000 0.630 0.630 srgb} bind def
-/col29 {1.000 0.750 0.750 srgb} bind def
-/col30 {1.000 0.880 0.880 srgb} bind def
-/col31 {1.000 0.840 0.000 srgb} bind def
-
-end
-save
--27.0 -15.0 translate
- 90 rotate
-1 -1 scale
-
-/cp {closepath} bind def
-/ef {eofill} bind def
-/gr {grestore} bind def
-/gs {gsave} bind def
-/sa {save} bind def
-/rs {restore} bind def
-/l {lineto} bind def
-/m {moveto} bind def
-/rm {rmoveto} bind def
-/n {newpath} bind def
-/s {stroke} bind def
-/sh {show} bind def
-/slc {setlinecap} bind def
-/slj {setlinejoin} bind def
-/slw {setlinewidth} bind def
-/srgb {setrgbcolor} bind def
-/rot {rotate} bind def
-/sc {scale} bind def
-/sd {setdash} bind def
-/ff {findfont} bind def
-/sf {setfont} bind def
-/scf {scalefont} bind def
-/sw {stringwidth} bind def
-/tr {translate} bind def
-/tnt {dup dup currentrgbcolor
- 4 -2 roll dup 1 exch sub 3 -1 roll mul add
- 4 -2 roll dup 1 exch sub 3 -1 roll mul add
- 4 -2 roll dup 1 exch sub 3 -1 roll mul add srgb}
- bind def
-/shd {dup dup currentrgbcolor 4 -2 roll mul 4 -2 roll mul
- 4 -2 roll mul srgb} bind def
- /DrawEllipse {
- /endangle exch def
- /startangle exch def
- /yrad exch def
- /xrad exch def
- /y exch def
- /x exch def
- /savematrix mtrx currentmatrix def
- x y tr xrad yrad sc 0 0 1 startangle endangle arc
- closepath
- savematrix setmatrix
- } def
-
-/$F2psBegin {$F2psDict begin /$F2psEnteredState save def} def
-/$F2psEnd {$F2psEnteredState restore end} def
-%%EndProlog
-
-$F2psBegin
-10 setmiterlimit
-n 0 612 m 0 0 l 792 0 l 792 612 l cp clip
- 0.04200 0.04200 sc
-7.500 slw
-% Ellipse
-n 8700 4200 165 165 0 360 DrawEllipse gs 0.00 setgray ef gr gs col-1 s gr
-
-% Ellipse
-n 17400 3300 165 165 0 360 DrawEllipse gs 0.00 setgray ef gr gs col-1 s gr
-
-% Ellipse
-n 14100 9000 210 210 0 360 DrawEllipse gs 0.00 setgray ef gr gs col-1 s gr
-
-% Ellipse
-n 10800 7800 165 165 0 360 DrawEllipse gs 0.00 setgray ef gr gs col-1 s gr
-
-% Ellipse
-n 11400 3000 165 165 0 360 DrawEllipse gs 0.00 setgray ef gr gs col-1 s gr
-
-% Ellipse
-n 5400 3000 165 165 0 360 DrawEllipse gs 0.00 setgray ef gr gs col-1 s gr
-
-% Ellipse
-n 14700 4200 165 165 0 360 DrawEllipse gs 0.00 setgray ef gr gs col-1 s gr
-
-% Ellipse
-n 6225 7050 165 165 0 360 DrawEllipse gs 0.00 setgray ef gr gs col-1 s gr
-
-% Ellipse
-n 3900 6000 165 165 0 360 DrawEllipse gs 0.00 setgray ef gr gs col-1 s gr
-
-% Ellipse
-n 4200 8700 165 165 0 360 DrawEllipse gs 0.00 setgray ef gr gs col-1 s gr
-
-% Ellipse
-n 5775 9750 165 165 0 360 DrawEllipse gs 0.00 setgray ef gr gs col-1 s gr
-
-% Polyline
-n 16500 1500 m 17400 3300 l 16500 4200 l gs 0.75 setgray ef gr gs col-1 s gr
-% Polyline
-n 6225 7050 m 5775 9750 l 7125 8850 l gs 0.75 setgray ef gr gs col-1 s gr
-% Polyline
-n 10800 7800 m 12000 9000 l 14100 9000 l gs 0.75 setgray ef gr gs col-1 s gr
-% Polyline
-n 3900 6000 m 2700 8100 l 4200 8700 l gs 0.75 setgray ef gr gs col-1 s gr
-% Polyline
-n 11400 3000 m 12600 4200 l 14700 4200 l gs 0.75 setgray ef gr gs col-1 s gr
-% Polyline
-n 5400 3000 m 6600 4200 l 8700 4200 l gs 0.75 setgray ef gr gs col-1 s gr
-/Times-Roman ff 450.00 scf sf
-3300 2700 m
-gs 1 -1 sc (b) col-1 sh gr
-/Times-Roman ff 450.00 scf sf
-10125 2700 m
-gs 1 -1 sc (b) col-1 sh gr
-% Polyline
-gs clippath
-15966 816 m 16042 698 l 16038 838 l 16090 672 l 16019 649 l cp clip
-n 15600 2100 m 16050 675 l gs 0.75 setgray ef gr gs col-1 s gr gr
-
-% arrowhead
-n 15966 816 m 16042 698 l 16038 838 l col-1 s
-/Times-Roman ff 450.00 scf sf
-375 3000 m
-gs 1 -1 sc (a) col-1 sh gr
-% Polyline
-n 12600 5775 m 13200 7275 l gs 0.00 setgray ef gr gs col-1 s gr
-% Polyline
-gs clippath
-12339 8545 m 12287 8675 l 12264 8538 l 12246 8711 l 12321 8719 l cp clip
-12531 5930 m 12582 5799 l 12606 5937 l 12624 5764 l 12549 5756 l cp clip
-n 12585 5775 m 12285 8700 l gs 0.00 setgray ef gr gs col-1 s gr gr
-
-% arrowhead
-n 12531 5930 m 12582 5799 l 12606 5937 l col-1 s
-% arrowhead
-n 12339 8545 m 12287 8675 l 12264 8538 l col-1 s
-% Polyline
-gs clippath
-12360 8603 m 12253 8694 l 12297 8562 l 12200 8707 l 12263 8748 l cp clip
-13020 7477 m 13126 7385 l 13083 7518 l 13180 7373 l 13117 7332 l cp clip
-n 13140 7365 m 12240 8715 l gs 0.00 setgray ef gr gs col-1 s gr gr
-
-% arrowhead
-n 13020 7477 m 13126 7385 l 13083 7518 l col-1 s
-% arrowhead
-n 12360 8603 m 12253 8694 l 12297 8562 l col-1 s
-% Polyline
-gs clippath
-6176 8539 m 6291 8617 l 6152 8610 l 6317 8665 l 6341 8594 l cp clip
-3754 7811 m 3638 7732 l 3778 7740 l 3613 7685 l 3589 7756 l cp clip
-n 3615 7725 m 6315 8625 l gs 0.00 setgray ef gr gs col-1 s gr gr
-
-% arrowhead
-n 3754 7811 m 3638 7732 l 3778 7740 l col-1 s
-% arrowhead
-n 6176 8539 m 6291 8617 l 6152 8610 l col-1 s
-% Polyline
-gs clippath
-12820 6668 m 12893 6548 l 12892 6688 l 12940 6521 l 12868 6500 l cp clip
-12380 8482 m 12306 8601 l 12308 8462 l 12260 8629 l 12332 8650 l cp clip
-n 12300 8625 m 12900 6525 l gs 0.75 setgray ef gr gs col-1 s gr gr
-
-% arrowhead
-n 12380 8482 m 12306 8601 l 12308 8462 l col-1 s
-% arrowhead
-n 12820 6668 m 12893 6548 l 12892 6688 l col-1 s
-/Symbol ff 450.00 scf sf
-8250 1200 m
-gs 1 -1 sc (f) col-1 sh gr
-/Times-Roman ff 450.00 scf sf
-13275 8175 m
-gs 1 -1 sc (2) col-1 sh gr
-/Times-Roman ff 675.00 scf sf
-11100 4800 m
-gs 1 -1 sc (C) col-1 sh gr
-/Times-Roman ff 675.00 scf sf
-1800 9600 m
-gs 1 -1 sc (D) col-1 sh gr
-/Times-Roman ff 450.00 scf sf
-4800 7950 m
-gs 1 -1 sc (d) col-1 sh gr
-/Times-Roman ff 450.00 scf sf
-13050 6675 m
-gs 1 -1 sc (d) col-1 sh gr
-/Times-Roman ff 675.00 scf sf
-10200 9600 m
-gs 1 -1 sc (E) col-1 sh gr
-/Symbol ff 450.00 scf sf
-15075 1425 m
-gs 1 -1 sc (f) col-1 sh gr
-/Times-Roman ff 450.00 scf sf
-13050 7950 m
-gs 1 -1 sc (d) col-1 sh gr
-/Symbol ff 450.00 scf sf
-1800 1275 m
-gs 1 -1 sc (f) col-1 sh gr
-/Times-Roman ff 675.00 scf sf
-1200 4800 m
-gs 1 -1 sc (A) col-1 sh gr
-/Times-Roman ff 675.00 scf sf
-5100 4800 m
-gs 1 -1 sc (B) col-1 sh gr
-/Times-Roman ff 450.00 scf sf
-6825 2475 m
-gs 1 -1 sc (n) col-1 sh gr
-/Times-Roman ff 450.00 scf sf
-12225 7050 m
-gs 1 -1 sc (1) col-1 sh gr
-/Times-Roman ff 450.00 scf sf
-12000 6825 m
-gs 1 -1 sc (d) col-1 sh gr
-/Times-Roman ff 450.00 scf sf
-15225 2925 m
-gs 1 -1 sc (n) col-1 sh gr
-/Times-Roman ff 450.00 scf sf
-12750 2250 m
-gs 1 -1 sc (n) col-1 sh gr
-% Polyline
-gs clippath
-8595 1326 m 8689 1221 l 8662 1359 l 8740 1203 l 8673 1170 l cp clip
-n 8100 2400 m 8700 1200 l gs col-1 s gr gr
-
-% arrowhead
-n 8595 1326 m 8689 1221 l 8662 1359 l col-1 s
-% Ellipse
-n 10200 1500 165 165 0 360 DrawEllipse gs 0.00 setgray ef gr gs col-1 s gr
-
-% Ellipse
-n 9300 3300 165 165 0 360 DrawEllipse gs 0.00 setgray ef gr gs col-1 s gr
-
-% Ellipse
-n 12600 5700 165 165 0 360 DrawEllipse gs 0.00 setgray ef gr gs col-1 s gr
-
-% Ellipse
-n 13200 7275 165 165 0 360 DrawEllipse gs 0.00 setgray ef gr gs col-1 s gr
-
-% Ellipse
-n 12000 9000 210 210 0 360 DrawEllipse gs 0.00 setgray ef gr gs col-1 s gr
-
-% Ellipse
-n 12600 4200 165 165 0 360 DrawEllipse gs 0.00 setgray ef gr gs col-1 s gr
-
-% Ellipse
-n 6600 4200 165 165 0 360 DrawEllipse gs 0.00 setgray ef gr gs col-1 s gr
-
-15.000 slw
-% Arc
-gs n 1875.0 1893.8 243.8 -157.4 -22.6 arc
-gs col-1 s gr
- gr
-
-% Arc
-gs n 8287.5 1762.5 191.2 -168.7 -11.3 arc
-gs col-1 s gr
- gr
-
-% Arc
-gs n 15633.3 2116.7 408.7 -73.4 -177.7 arcn
-gs col-1 s gr
- gr
-
-7.500 slw
-% Ellipse
-n 600 1500 165 165 0 360 DrawEllipse gs 0.00 setgray ef gr gs col-1 s gr
-
-% Ellipse
-n 1200 3600 165 165 0 360 DrawEllipse gs 0.00 setgray ef gr gs col-1 s gr
-
-% Ellipse
-n 2400 3300 165 165 0 360 DrawEllipse gs 0.00 setgray ef gr gs col-1 s gr
-
-% Ellipse
-n 3300 1500 165 165 0 360 DrawEllipse gs 0.00 setgray ef gr gs col-1 s gr
-
-% Ellipse
-n 16500 4200 165 165 0 360 DrawEllipse gs 0.00 setgray ef gr gs col-1 s gr
-
-% Polyline
-gs clippath
-2295 1326 m 2389 1221 l 2362 1359 l 2440 1203 l 2373 1170 l cp clip
-n 1800 2400 m 2400 1200 l gs col-1 s gr gr
-
-% arrowhead
-n 2295 1326 m 2389 1221 l 2362 1359 l col-1 s
-% Polyline
-gs clippath
-8063 1359 m 8100 1224 l 8138 1359 l 8138 1185 l 8063 1185 l cp clip
-n 8100 2400 m 8100 1200 l gs col-1 s gr gr
-
-% arrowhead
-n 8063 1359 m 8100 1224 l 8138 1359 l col-1 s
-% Polyline
-gs clippath
-7302 1569 m 7373 1448 l 7375 1589 l 7420 1420 l 7348 1401 l cp clip
-n 6750 3750 m 7380 1425 l gs 0.75 setgray ef gr gs col-1 s gr gr
-
-% arrowhead
-n 7302 1569 m 7373 1448 l 7375 1589 l col-1 s
-% Polyline
-gs clippath
-13489 1639 m 13567 1523 l 13560 1663 l 13615 1498 l 13544 1474 l cp clip
-n 12825 3750 m 13575 1500 l gs 0.75 setgray ef gr gs col-1 s gr gr
-
-% arrowhead
-n 13489 1639 m 13567 1523 l 13560 1663 l col-1 s
-% Polyline
-gs clippath
-14559 3113 m 14424 3075 l 14559 3038 l 14385 3038 l 14385 3113 l cp clip
-n 16725 3075 m 14400 3075 l gs 0.75 setgray ef gr gs col-1 s gr gr
-
-% arrowhead
-n 14559 3113 m 14424 3075 l 14559 3038 l col-1 s
-% Polyline
-gs clippath
-14184 2138 m 14049 2100 l 14184 2063 l 14010 2063 l 14010 2138 l cp clip
-n 15600 2100 m 14025 2100 l gs 0.75 setgray ef gr gs col-1 s gr gr
-
-% arrowhead
-n 14184 2138 m 14049 2100 l 14184 2063 l col-1 s
-% Polyline
-gs clippath
-1502 1364 m 1505 1223 l 1575 1345 l 1533 1176 l 1460 1195 l cp clip
-n 1800 2400 m 1500 1200 l gs col-1 s gr gr
-
-% arrowhead
-n 1502 1364 m 1505 1223 l 1575 1345 l col-1 s
-% Ellipse
-n 16500 1500 165 165 0 360 DrawEllipse gs 0.00 setgray ef gr gs col-1 s gr
-
-% Ellipse
-n 2700 8100 165 165 0 360 DrawEllipse gs 0.00 setgray ef gr gs col-1 s gr
-
-% Ellipse
-n 7125 8850 165 165 0 360 DrawEllipse gs 0.00 setgray ef gr gs col-1 s gr
-
-% Ellipse
-n 6600 4200 165 165 0 360 DrawEllipse gs 0.00 setgray ef gr gs col-1 s gr
-
-% Polyline
-n 600 1500 m 1200 3600 l gs 0.00 setgray ef gr gs col-1 s gr
-% Polyline
-n 2400 3300 m 3300 1500 l gs 0.00 setgray ef gr gs col-1 s gr
-% Polyline
-n 9300 3300 m 10200 1500 l gs 0.75 setgray ef gr gs col-1 s gr
-$F2psEnd
-rs
+++ /dev/null
-#FIG 3.1
-Landscape
-Center
-Inches
-1200 2
-5 1 0 2 -1 -1 0 0 -1 0.000 0 0 0 0 1875.000 1893.750 1650 1800 1875 1650 2100 1800
-5 1 0 2 -1 -1 0 0 -1 0.000 0 0 0 0 8287.500 1762.500 8100 1725 8325 1575 8475 1725
-5 1 0 2 -1 -1 0 0 -1 0.000 0 1 0 0 15633.331 2116.665 15750 1725 15375 1800 15225 2100
-1 3 0 1 -1 -1 0 0 20 0.000 1 0.0000 600 1500 165 165 600 1500 750 1575
-1 3 0 1 -1 -1 0 0 20 0.000 1 0.0000 1200 3600 165 165 1200 3600 1350 3675
-1 3 0 1 -1 -1 0 0 20 0.000 1 0.0000 2400 3300 165 165 2400 3300 2550 3375
-1 3 0 1 -1 -1 0 0 20 0.000 1 0.0000 3300 1500 165 165 3300 1500 3450 1575
-1 3 0 1 -1 -1 0 0 20 0.000 1 0.0000 6600 4200 165 165 6600 4200 6750 4275
-1 3 0 1 -1 -1 2 0 20 0.000 1 0.0000 8700 4200 165 165 8700 4200 8865 4365
-1 3 0 1 -1 -1 0 0 20 0.000 1 0.0000 10200 1500 165 165 10200 1500 10350 1575
-1 3 0 1 -1 -1 0 0 20 0.000 1 0.0000 9300 3300 165 165 9300 3300 9450 3375
-1 3 0 1 -1 -1 0 0 20 0.000 1 0.0000 12600 5700 165 165 12600 5700 12675 5850
-1 3 0 1 -1 -1 0 0 20 0.000 1 0.0000 13200 7275 165 165 13200 7275 13275 7425
-1 3 0 1 -1 -1 0 0 20 0.000 1 0.0000 12000 9000 210 210 12000 9000 12150 9150
-1 3 0 1 -1 -1 2 0 20 0.000 1 0.0000 14100 9000 210 210 14100 9000 14310 9210
-1 3 0 1 -1 -1 2 0 20 0.000 1 0.0000 10800 7800 165 165 10800 7800 10965 7965
-1 3 0 1 -1 -1 2 0 20 0.000 1 0.0000 11400 3000 165 165 11400 3000 11565 3165
-1 3 0 1 -1 -1 0 0 20 0.000 1 0.0000 12600 4200 165 165 12600 4200 12675 4350
-1 3 0 1 -1 -1 2 0 20 0.000 1 0.0000 14700 4200 165 165 14700 4200 14865 4365
-1 3 0 1 -1 -1 0 0 20 0.000 1 0.0000 16500 4200 165 165 16500 4200 16650 4275
-1 3 0 1 -1 -1 2 0 20 0.000 1 0.0000 17400 3300 165 165 17400 3300 17565 3465
-1 3 0 1 -1 -1 0 0 20 0.000 1 0.0000 16500 1500 165 165 16500 1500 16575 1650
-1 3 0 1 -1 -1 2 0 20 0.000 1 0.0000 3900 6000 165 165 3900 6000 4065 6165
-1 3 0 1 -1 -1 0 0 20 0.000 1 0.0000 2700 8100 165 165 2700 8100 2775 8250
-1 3 0 1 -1 -1 2 0 20 0.000 1 0.0000 4200 8700 165 165 4200 8700 4365 8865
-1 3 0 1 -1 -1 2 0 20 0.000 1 0.0000 6225 7050 165 165 6225 7050 6390 7215
-1 3 0 1 -1 -1 2 0 20 0.000 1 0.0000 5775 9750 165 165 5775 9750 5940 9915
-1 3 0 1 -1 -1 0 0 20 0.000 1 0.0000 7125 8850 165 165 7125 8850 7290 9015
-1 3 0 1 -1 -1 0 0 20 0.000 1 0.0000 6600 4200 165 165 6600 4200 6675 4350
-1 3 0 1 -1 -1 2 0 20 0.000 1 0.0000 5400 3000 165 165 5400 3000 5565 3165
-2 1 0 1 -1 -1 0 0 20 0.000 0 0 -1 0 0 2
- 600 1500 1200 3600
-2 1 0 1 -1 -1 0 0 20 0.000 0 0 -1 0 0 2
- 2400 3300 3300 1500
-2 1 0 1 -1 -1 0 0 5 0.000 0 0 -1 0 0 2
- 9300 3300 10200 1500
-2 1 0 1 -1 -1 0 0 -1 0.000 0 0 -1 1 0 2
- 0 0 1.00 75.00 135.00
- 1800 2400 1500 1200
-2 1 0 1 -1 -1 0 0 -1 0.000 0 0 -1 1 0 2
- 0 0 1.00 75.00 135.00
- 1800 2400 2400 1200
-2 1 0 1 -1 -1 0 0 -1 0.000 0 0 -1 1 0 2
- 0 0 1.00 75.00 135.00
- 8100 2400 8100 1200
-2 1 0 1 -1 -1 0 0 -1 0.000 0 0 -1 1 0 2
- 0 0 1.00 75.00 135.00
- 8100 2400 8700 1200
-2 1 0 1 -1 -1 0 0 5 0.000 0 0 -1 1 0 2
- 0 0 1.00 75.00 135.00
- 6750 3750 7380 1425
-2 1 0 1 -1 -1 1 0 5 0.000 0 0 -1 0 0 3
- 11400 3000 12600 4200 14700 4200
-2 1 0 1 -1 -1 1 0 5 0.000 0 0 -1 0 0 3
- 16500 1500 17400 3300 16500 4200
-2 1 0 1 -1 -1 0 0 5 0.000 0 0 -1 1 0 2
- 0 0 1.00 75.00 135.00
- 12825 3750 13575 1500
-2 1 0 1 -1 -1 0 0 5 0.000 0 0 -1 1 0 2
- 0 0 1.00 75.00 135.00
- 16725 3075 14400 3075
-2 1 0 1 -1 -1 0 0 5 0.000 0 0 -1 1 0 2
- 0 0 1.00 75.00 135.00
- 15600 2100 14025 2100
-2 1 0 1 -1 -1 0 0 5 0.000 0 0 -1 1 0 2
- 0 0 1.00 75.00 135.00
- 15600 2100 16050 675
-2 1 0 1 -1 -1 0 0 20 0.000 0 0 -1 0 0 2
- 12600 5775 13200 7275
-2 1 0 1 -1 -1 1 0 5 0.000 0 0 -1 0 0 3
- 10800 7800 12000 9000 14100 9000
-2 1 0 1 -1 -1 0 0 20 0.000 0 0 -1 1 1 2
- 0 0 1.00 75.00 135.00
- 0 0 1.00 75.00 135.00
- 12585 5775 12285 8700
-2 1 0 1 -1 -1 0 0 20 0.000 0 0 -1 1 1 2
- 0 0 1.00 75.00 135.00
- 0 0 1.00 75.00 135.00
- 13140 7365 12240 8715
-2 1 0 1 -1 -1 1 0 5 0.000 0 0 -1 0 0 3
- 3900 6000 2700 8100 4200 8700
-2 1 0 1 -1 -1 1 0 5 0.000 0 0 -1 0 0 3
- 6225 7050 5775 9750 7125 8850
-2 1 0 1 -1 -1 0 0 20 0.000 0 0 -1 1 1 2
- 0 0 1.00 75.00 135.00
- 0 0 1.00 75.00 135.00
- 3615 7725 6315 8625
-2 1 0 1 -1 -1 0 0 5 0.000 0 0 -1 1 1 2
- 0 0 1.00 75.00 135.00
- 0 0 1.00 75.00 135.00
- 12300 8625 12900 6525
-2 1 0 1 -1 -1 1 0 5 0.000 0 0 -1 0 0 3
- 5400 3000 6600 4200 8700 4200
-4 0 -1 0 0 0 30 0.0000 0 195 195 375 3000 a\001
-4 0 -1 0 0 0 30 0.0000 0 300 225 3300 2700 b\001
-4 0 -1 0 0 0 30 0.0000 0 300 225 10125 2700 b\001
-4 0 -1 0 0 32 30 0.0000 4 405 240 1800 1275 f\001
-4 0 -1 0 0 32 30 0.0000 4 405 240 8250 1200 f\001
-4 0 -1 0 0 0 45 0.0000 0 465 480 1200 4800 A\001
-4 0 -1 0 0 0 45 0.0000 0 450 450 5100 4800 B\001
-4 0 -1 0 0 0 30 0.0000 0 195 225 6825 2475 n\001
-4 0 -1 0 0 0 30 0.0000 0 195 225 12750 2250 n\001
-4 0 -1 0 0 0 30 0.0000 0 195 225 15225 2925 n\001
-4 0 -1 0 0 0 30 0.0000 0 300 225 12000 6825 d\001
-4 0 -1 0 0 0 30 0.0000 0 300 225 12225 7050 1\001
-4 0 -1 0 0 0 30 0.0000 0 300 225 13050 7950 d\001
-4 0 -1 0 0 0 30 0.0000 0 300 225 13275 8175 2\001
-4 0 -1 0 0 0 45 0.0000 0 480 450 11100 4800 C\001
-4 0 -1 0 0 0 45 0.0000 0 450 480 1800 9600 D\001
-4 0 -1 0 0 0 30 0.0000 0 300 225 4800 7950 d\001
-4 0 -1 0 0 0 30 0.0000 0 300 225 13050 6675 d\001
-4 0 -1 0 0 0 45 0.0000 0 450 405 10200 9600 E\001
-4 0 -1 0 0 32 30 0.0000 4 405 240 15075 1425 f\001
--- /dev/null
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<!-- Created with Inkscape (http://www.inkscape.org/) -->
+
+<svg
+ xmlns:dc="http://purl.org/dc/elements/1.1/"
+ xmlns:cc="http://creativecommons.org/ns#"
+ xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+ xmlns:svg="http://www.w3.org/2000/svg"
+ xmlns="http://www.w3.org/2000/svg"
+ xmlns:sodipodi="http://sodipodi.sourceforge.net/DTD/sodipodi-0.dtd"
+ xmlns:inkscape="http://www.inkscape.org/namespaces/inkscape"
+ id="svg3074"
+ version="1.1"
+ inkscape:version="0.48.2 r9819"
+ width="449.44434"
+ height="99.803299"
+ xml:space="preserve"
+ sodipodi:docname="sgangle.svg"><metadata
+ id="metadata3080"><rdf:RDF><cc:Work
+ rdf:about=""><dc:format>image/svg+xml</dc:format><dc:type
+ rdf:resource="http://purl.org/dc/dcmitype/StillImage" /><dc:title></dc:title></cc:Work></rdf:RDF></metadata><defs
+ id="defs3078"><marker
+ inkscape:stockid="Arrow1Mend"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="Arrow1Mend"
+ style="overflow:visible"><path
+ id="path4597"
+ d="M 0,0 5,-5 -12.5,0 5,5 0,0 z"
+ style="fill-rule:evenodd;stroke:#000000;stroke-width:1pt;marker-start:none"
+ transform="matrix(-0.4,0,0,-0.4,-4,0)"
+ inkscape:connector-curvature="0" /></marker><marker
+ inkscape:stockid="Arrow1Mstart"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="Arrow1Mstart"
+ style="overflow:visible"><path
+ id="path4594"
+ d="M 0,0 5,-5 -12.5,0 5,5 0,0 z"
+ style="fill-rule:evenodd;stroke:#000000;stroke-width:1pt;marker-start:none"
+ transform="matrix(0.4,0,0,0.4,4,0)"
+ inkscape:connector-curvature="0" /></marker><marker
+ inkscape:stockid="Arrow1Lend"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="Arrow1Lend"
+ style="overflow:visible"><path
+ id="path4591"
+ d="M 0,0 5,-5 -12.5,0 5,5 0,0 z"
+ style="fill-rule:evenodd;stroke:#000000;stroke-width:1pt;marker-start:none"
+ transform="matrix(-0.8,0,0,-0.8,-10,0)"
+ inkscape:connector-curvature="0" /></marker><marker
+ inkscape:stockid="Arrow1Lstart"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="Arrow1Lstart"
+ style="overflow:visible"><path
+ id="path4588"
+ d="M 0,0 5,-5 -12.5,0 5,5 0,0 z"
+ style="fill-rule:evenodd;stroke:#000000;stroke-width:1pt;marker-start:none"
+ transform="matrix(0.8,0,0,0.8,10,0)"
+ inkscape:connector-curvature="0" /></marker><marker
+ inkscape:stockid="DotL"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="DotL"
+ style="overflow:visible"><path
+ id="path4650"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ style="fill-rule:evenodd;stroke:#000000;stroke-width:1pt;marker-start:none;marker-end:none"
+ transform="matrix(0.8,0,0,0.8,5.92,0.8)"
+ inkscape:connector-curvature="0" /></marker><clipPath
+ clipPathUnits="userSpaceOnUse"
+ id="clipPath3164"><path
+ d="m 0,0 0,7240 3900,0 L 3900,0 0,0 z m 72.7188,6555.72 -49.5586,31.92 58.8007,-1.68 -69.7226,21.84 -9.66018,-29.82 70.14068,-22.26 z"
+ id="path3166"
+ inkscape:connector-curvature="0" /></clipPath><clipPath
+ clipPathUnits="userSpaceOnUse"
+ id="clipPath3188"><path
+ d="m 0,0 0,7240 3900,0 L 3900,0 0,0 z m 3318.9,5032.38 54.6,-21.84 -57.54,-9.66 72.66,-7.56 3.36,31.5 -73.08,7.56 z"
+ id="path3190"
+ inkscape:connector-curvature="0" /></clipPath><clipPath
+ clipPathUnits="userSpaceOnUse"
+ id="clipPath3194"><path
+ d="m 0,0 0,7240 3900,0 L 3900,0 0,0 z m 3318.9,5032.38 54.6,-21.84 -57.54,-9.66 72.66,-7.56 3.36,31.5 -73.08,7.56 z m -1098.3,80.64 -55.02,21.42 57.96,10.08 -72.66,7.56 -3.36,-31.5 73.08,-7.56 z"
+ id="path3196"
+ inkscape:connector-curvature="0" /></clipPath><clipPath
+ clipPathUnits="userSpaceOnUse"
+ id="clipPath3210"><path
+ d="m 0,0 0,7240 3900,0 L 3900,0 0,0 z m 3343.26,5041.2 38.22,-44.94 -55.44,18.48 60.9,-40.74 17.22,26.46 -60.9,40.74 z"
+ id="path3212"
+ inkscape:connector-curvature="0" /></clipPath><clipPath
+ clipPathUnits="userSpaceOnUse"
+ id="clipPath3216"><path
+ d="m 0,0 0,7240 3900,0 L 3900,0 0,0 z m 3343.26,5041.2 38.22,-44.94 -55.44,18.48 60.9,-40.74 17.22,26.46 -60.9,40.74 z m -472.92,277.2 -38.64,44.52 55.86,-18.06 -60.9,40.74 -17.22,-26.46 60.9,-40.74 z"
+ id="path3218"
+ inkscape:connector-curvature="0" /></clipPath><clipPath
+ clipPathUnits="userSpaceOnUse"
+ id="clipPath3232"><path
+ d="m 0,0 0,7240 3900,0 L 3900,0 0,0 z m 3316.38,2443.92 32.76,48.3 -2.94,-58.38 23.1,69.3 -29.82,10.08 -23.1,-69.3 z"
+ id="path3234"
+ inkscape:connector-curvature="0" /></clipPath><clipPath
+ clipPathUnits="userSpaceOnUse"
+ id="clipPath3238"><path
+ d="m 0,0 0,7240 3900,0 L 3900,0 0,0 z m 3316.38,2443.92 32.76,48.3 -2.94,-58.38 23.1,69.3 -29.82,10.08 -23.1,-69.3 z m -305.76,-1017.24 -33.18,-48.72 3.36,58.8 -23.1,-69.3 29.82,-10.08 23.1,69.3 z"
+ id="path3240"
+ inkscape:connector-curvature="0" /></clipPath><clipPath
+ clipPathUnits="userSpaceOnUse"
+ id="clipPath3254"><path
+ d="m 0,0 0,7240 3900,0 L 3900,0 0,0 z m 2530.56,5234.4 -50.4,30.66 58.8,-0.42 -70.14,20.16 -8.82,-30.24 70.56,-20.16 z"
+ id="path3256"
+ inkscape:connector-curvature="0" /></clipPath><clipPath
+ clipPathUnits="userSpaceOnUse"
+ id="clipPath3260"><path
+ d="m 0,0 0,7240 3900,0 L 3900,0 0,0 z m 2530.56,5234.4 -50.4,30.66 58.8,-0.42 -70.14,20.16 -8.82,-30.24 70.56,-20.16 z m 761.88,-184.8 49.98,-31.08 -58.38,0.84 70.14,-20.16 8.82,30.24 -70.56,20.16 z"
+ id="path3262"
+ inkscape:connector-curvature="0" /></clipPath><clipPath
+ clipPathUnits="userSpaceOnUse"
+ id="clipPath3330"><path
+ d="m 0,0 0,7240 3900,0 L 3900,0 0,0 z m 286.922,3459.9 -44.102,39.48 57.961,-11.34 -65.519,32.76 -13.864,-28.14 65.524,-32.76 z"
+ id="path3332"
+ inkscape:connector-curvature="0" /></clipPath><clipPath
+ clipPathUnits="userSpaceOnUse"
+ id="clipPath3396"><path
+ d="m 0,0 0,7240 3900,0 L 3900,0 0,0 z m 286.922,813.898 -44.102,39.481 57.961,-11.34 -65.519,32.762 -13.864,-28.141 65.524,-32.762 z"
+ id="path3398"
+ inkscape:connector-curvature="0" /></clipPath><clipPath
+ clipPathUnits="userSpaceOnUse"
+ id="clipPath3408"><path
+ d="m 0,0 0,7240 3900,0 L 3900,0 0,0 z m 300.781,3236.46 -56.703,15.54 56.703,15.96 -73.082,0 0,-31.5 73.082,0 z"
+ id="path3410"
+ inkscape:connector-curvature="0" /></clipPath><clipPath
+ clipPathUnits="userSpaceOnUse"
+ id="clipPath3420"><path
+ d="m 0,0 0,7240 3900,0 L 3900,0 0,0 z m 388.98,2916.84 -50.82,29.82 59.219,0.84 -70.981,18.9 -7.976,-30.24 70.558,-19.32 z"
+ id="path3422"
+ inkscape:connector-curvature="0" /></clipPath><clipPath
+ clipPathUnits="userSpaceOnUse"
+ id="clipPath3434"><path
+ d="m 0,0 0,7240 3900,0 L 3900,0 0,0 z m 418.379,5515.38 -48.719,32.76 58.801,-2.94 -69.301,23.1 -10.082,-29.82 69.301,-23.1 z"
+ id="path3436"
+ inkscape:connector-curvature="0" /></clipPath><clipPath
+ clipPathUnits="userSpaceOnUse"
+ id="clipPath3448"><path
+ d="m 0,0 0,7240 3900,0 L 3900,0 0,0 z m 1037.46,5964.78 -15.96,-56.7 -15.54,56.7 0,-73.08 31.5,0 0,73.08 z"
+ id="path3450"
+ inkscape:connector-curvature="0" /></clipPath><clipPath
+ clipPathUnits="userSpaceOnUse"
+ id="clipPath3462"><path
+ d="m 0,0 0,7240 3900,0 L 3900,0 0,0 z m 627.961,5807.28 -15.961,-56.7 -15.539,56.7 0,-73.08 31.5,0 0,73.08 z"
+ id="path3464"
+ inkscape:connector-curvature="0" /></clipPath><clipPath
+ clipPathUnits="userSpaceOnUse"
+ id="clipPath3476"><path
+ d="m 0,0 0,7240 3900,0 L 3900,0 0,0 z m 302.879,480.84 -59.219,1.262 51.238,29.398 -70.976,-17.641 7.976,-30.66 70.981,17.641 z"
+ id="path3478"
+ inkscape:connector-curvature="0" /></clipPath><marker
+ inkscape:stockid="DotL"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="DotL-3"
+ style="overflow:visible"><path
+ id="path4650-2"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ style="fill-rule:evenodd;stroke:#000000;stroke-width:1pt;marker-start:none;marker-end:none"
+ transform="matrix(0.8,0,0,0.8,5.92,0.8)"
+ inkscape:connector-curvature="0" /></marker><marker
+ inkscape:stockid="DotL"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="marker8876"
+ style="overflow:visible"><path
+ id="path8878"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ style="fill-rule:evenodd;stroke:#000000;stroke-width:1pt;marker-start:none;marker-end:none"
+ transform="matrix(0.8,0,0,0.8,5.92,0.8)"
+ inkscape:connector-curvature="0" /></marker><marker
+ inkscape:stockid="DotL"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="marker8880"
+ style="overflow:visible"><path
+ id="path8882"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ style="fill-rule:evenodd;stroke:#000000;stroke-width:1pt;marker-start:none;marker-end:none"
+ transform="matrix(0.8,0,0,0.8,5.92,0.8)"
+ inkscape:connector-curvature="0" /></marker><marker
+ inkscape:stockid="Arrow1Mend"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="Arrow1Mend-5"
+ style="overflow:visible"><path
+ inkscape:connector-curvature="0"
+ id="path4597-9"
+ d="M 0,0 5,-5 -12.5,0 5,5 0,0 z"
+ style="fill-rule:evenodd;stroke:#000000;stroke-width:1pt;marker-start:none"
+ transform="matrix(-0.4,0,0,-0.4,-4,0)" /></marker><marker
+ inkscape:stockid="DotL"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="DotL-6"
+ style="overflow:visible"><path
+ id="path4650-4"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ style="fill-rule:evenodd;stroke:#000000;stroke-width:1pt;marker-start:none;marker-end:none"
+ transform="matrix(0.8,0,0,0.8,5.92,0.8)"
+ inkscape:connector-curvature="0" /></marker><marker
+ inkscape:stockid="DotL"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="marker9561"
+ style="overflow:visible"><path
+ id="path9563"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ style="fill-rule:evenodd;stroke:#000000;stroke-width:1pt;marker-start:none;marker-end:none"
+ transform="matrix(0.8,0,0,0.8,5.92,0.8)"
+ inkscape:connector-curvature="0" /></marker><marker
+ inkscape:stockid="DotL"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="marker9565"
+ style="overflow:visible"><path
+ id="path9567"
+ d="m -2.5,-1 c 0,2.76 -2.24,5 -5,5 -2.76,0 -5,-2.24 -5,-5 0,-2.76 2.24,-5 5,-5 2.76,0 5,2.24 5,5 z"
+ style="fill-rule:evenodd;stroke:#000000;stroke-width:1pt;marker-start:none;marker-end:none"
+ transform="matrix(0.8,0,0,0.8,5.92,0.8)"
+ inkscape:connector-curvature="0" /></marker><marker
+ inkscape:stockid="Arrow1Mend"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="Arrow1Mend-7"
+ style="overflow:visible"><path
+ inkscape:connector-curvature="0"
+ id="path4597-5"
+ d="M 0,0 5,-5 -12.5,0 5,5 0,0 z"
+ style="fill-rule:evenodd;stroke:#000000;stroke-width:1pt;marker-start:none"
+ transform="matrix(-0.4,0,0,-0.4,-4,0)" /></marker><marker
+ inkscape:stockid="Arrow1Mstart"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="Arrow1Mstart-2"
+ style="overflow:visible"><path
+ inkscape:connector-curvature="0"
+ id="path4594-0"
+ d="M 0,0 5,-5 -12.5,0 5,5 0,0 z"
+ style="fill-rule:evenodd;stroke:#000000;stroke-width:1pt;marker-start:none"
+ transform="matrix(0.4,0,0,0.4,4,0)" /></marker><marker
+ inkscape:stockid="Arrow1Mend"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="Arrow1Mend-0"
+ style="overflow:visible"><path
+ inkscape:connector-curvature="0"
+ id="path4597-1"
+ d="M 0,0 5,-5 -12.5,0 5,5 0,0 z"
+ style="fill-rule:evenodd;stroke:#000000;stroke-width:1pt;marker-start:none"
+ transform="matrix(-0.4,0,0,-0.4,-4,0)" /></marker><marker
+ inkscape:stockid="Arrow1Mstart"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="Arrow1Mstart-3"
+ style="overflow:visible"><path
+ inkscape:connector-curvature="0"
+ id="path4594-8"
+ d="M 0,0 5,-5 -12.5,0 5,5 0,0 z"
+ style="fill-rule:evenodd;stroke:#000000;stroke-width:1pt;marker-start:none"
+ transform="matrix(0.4,0,0,0.4,4,0)" /></marker><marker
+ inkscape:stockid="Arrow1Mend"
+ orient="auto"
+ refY="0"
+ refX="0"
+ id="Arrow1Mend-3"
+ style="overflow:visible"><path
+ inkscape:connector-curvature="0"
+ id="path4597-4"
+ d="M 0,0 5,-5 -12.5,0 5,5 0,0 z"
+ style="fill-rule:evenodd;stroke:#000000;stroke-width:1pt;marker-start:none"
+ transform="matrix(-0.4,0,0,-0.4,-4,0)" /></marker></defs><sodipodi:namedview
+ pagecolor="#ffffff"
+ bordercolor="#666666"
+ borderopacity="1"
+ objecttolerance="10"
+ gridtolerance="10"
+ guidetolerance="10"
+ inkscape:pageopacity="0"
+ inkscape:pageshadow="2"
+ inkscape:window-width="1227"
+ inkscape:window-height="700"
+ id="namedview3076"
+ showgrid="true"
+ inkscape:snap-global="true"
+ fit-margin-top="0"
+ fit-margin-left="0"
+ fit-margin-right="0"
+ fit-margin-bottom="0"
+ inkscape:zoom="2"
+ inkscape:cx="265.31953"
+ inkscape:cy="75.132976"
+ inkscape:window-x="44"
+ inkscape:window-y="6"
+ inkscape:window-maximized="0"
+ inkscape:current-layer="g3082"
+ units="mm"
+ inkscape:object-paths="true"
+ inkscape:snap-intersection-paths="false"><inkscape:grid
+ type="xygrid"
+ id="grid3691"
+ empspacing="5"
+ visible="true"
+ enabled="true"
+ snapvisiblegridlinesonly="true" /></sodipodi:namedview><g
+ id="g3082"
+ inkscape:groupmode="layer"
+ inkscape:label="ink_ext_XXXXXX"
+ transform="matrix(0,1.25,1.25,0,-1515.0162,-399.1308)"><path
+ style="fill:none;stroke:#000000;stroke-width:1;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-opacity:1;stroke-dasharray:none;marker-start:url(#DotL);marker-end:url(#DotL)"
+ d="m 56.2485,431.35741 -20,-60"
+ id="path3815"
+ inkscape:connector-curvature="0"
+ transform="matrix(0,0.8,0.8,0,41.880103,1194.9892)"
+ sodipodi:nodetypes="cc" /><path
+ style="fill:none;stroke:#000000;stroke-width:1;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-opacity:1;stroke-dasharray:none;marker-start:url(#DotL);marker-end:url(#DotL)"
+ d="m 81.2485,421.35741 20,-60"
+ id="path5211"
+ inkscape:connector-curvature="0"
+ transform="matrix(0,0.8,0.8,0,41.880103,1194.9892)"
+ sodipodi:nodetypes="cc" /><g
+ id="g8666"
+ transform="translate(24,-12)"><path
+ sodipodi:nodetypes="ccc"
+ inkscape:connector-curvature="0"
+ id="path5759"
+ d="m 310.96603,1251.988 24,8 -24,8"
+ style="fill:none;stroke:#000000;stroke-width:0.80000001px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1;marker-start:url(#Arrow1Mstart);marker-end:url(#Arrow1Mend)" /><path
+ sodipodi:open="true"
+ sodipodi:end="5.060828"
+ sodipodi:start="4.381757"
+ transform="matrix(0,0.8,0.8,0,41.880104,1195.988)"
+ d="m 73.787564,347.39388 c 4.13685,-1.41989 8.635264,-1.37984 12.746175,0.11349"
+ sodipodi:ry="19.136335"
+ sodipodi:rx="19.136335"
+ sodipodi:cy="365.49374"
+ sodipodi:cx="80"
+ id="path6322"
+ style="fill:none;stroke:#000000;stroke-width:1;stroke-miterlimit:4;stroke-opacity:1;stroke-dasharray:none;marker-start:none"
+ sodipodi:type="arc" /></g><text
+ xml:space="preserve"
+ style="font-size:12.80000019px;font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;text-align:start;line-height:125%;letter-spacing:0px;word-spacing:0px;writing-mode:lr-tb;text-anchor:start;fill:#000000;fill-opacity:1;stroke:none;font-family:Sans;-inkscape-font-specification:Sans"
+ x="1211.913"
+ y="398.96603"
+ id="text6324"
+ sodipodi:linespacing="125%"
+ transform="matrix(0,1,1,0,0,0)"><tspan
+ sodipodi:role="line"
+ id="tspan6326"
+ x="1211.913"
+ y="398.96603">A</tspan></text>
+<g
+ id="g8860"
+ transform="translate(8.0000004,-16)"><path
+ sodipodi:nodetypes="ccc"
+ inkscape:connector-curvature="0"
+ id="path6328"
+ d="m 358.96603,1311.988 24,24 0,36"
+ style="fill:#c0c0c0;fill-opacity:1;stroke:#000000;stroke-width:0.80000001px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1;marker-start:url(#DotL);marker-mid:url(#DotL);marker-end:url(#DotL)" /><path
+ sodipodi:nodetypes="cc"
+ inkscape:connector-curvature="0"
+ id="path6888"
+ d="m 374.96603,1339.988 -24,8"
+ style="fill:none;stroke:#000000;stroke-width:0.80000001px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1;marker-end:url(#Arrow1Mend)" /></g><text
+ xml:space="preserve"
+ style="font-size:12.80000019px;font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;text-align:start;line-height:125%;letter-spacing:0px;word-spacing:0px;writing-mode:lr-tb;text-anchor:start;fill:#000000;fill-opacity:1;stroke:none;font-family:Sans;-inkscape-font-specification:Sans"
+ x="1287.988"
+ y="398.96603"
+ id="text6324-0"
+ sodipodi:linespacing="125%"
+ transform="matrix(0,1,1,0,0,0)"><tspan
+ sodipodi:role="line"
+ id="tspan7507"
+ x="1287.988"
+ y="398.96603">B</tspan></text>
+<g
+ transform="matrix(0,1,-1,0,1698.954,1013.022)"
+ id="g8860-5"><path
+ sodipodi:nodetypes="ccc"
+ inkscape:connector-curvature="0"
+ id="path6328-6"
+ d="m 358.96603,1311.988 24,24 0,36"
+ style="fill:#c0c0c0;fill-opacity:1;stroke:#000000;stroke-width:0.80000001px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1;marker-start:url(#DotL);marker-mid:url(#DotL);marker-end:url(#DotL)" /><path
+ sodipodi:nodetypes="cc"
+ inkscape:connector-curvature="0"
+ id="path6888-3"
+ d="m 374.96603,1339.988 -24,8"
+ style="fill:none;stroke:#000000;stroke-width:0.80000001px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1;marker-end:url(#Arrow1Mend)" /></g><g
+ id="g9520"
+ transform="translate(11.999998,168)"><path
+ sodipodi:nodetypes="ccc"
+ transform="matrix(0,0.8,0.8,0,285.87509,1211.988)"
+ inkscape:connector-curvature="0"
+ id="path8916"
+ d="m 165,41.363678 10,30 20,-20"
+ style="fill:none;stroke:#000000;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1;marker-start:url(#Arrow1Mstart);marker-end:url(#Arrow1Mend-5)" /><path
+ sodipodi:end="5.4889046"
+ sodipodi:start="4.3931718"
+ transform="matrix(0,0.8,0.8,0,285.87509,1211.988)"
+ d="m 168.72353,52.37405 c 7.11471,-2.35156 14.94704,-0.528828 20.29243,4.722434"
+ sodipodi:ry="20"
+ sodipodi:rx="20"
+ sodipodi:cy="71.363678"
+ sodipodi:cx="175"
+ id="path9518"
+ style="fill:none;stroke:#000000;stroke-width:1;stroke-miterlimit:4;stroke-opacity:1;stroke-dasharray:none"
+ sodipodi:type="arc"
+ sodipodi:open="true" /></g><g
+ id="g8860-52"
+ transform="translate(4.0000004,108)"><path
+ sodipodi:nodetypes="ccc"
+ inkscape:connector-curvature="0"
+ id="path6328-0"
+ d="m 358.96603,1311.988 24,24 0,36"
+ style="fill:#c0c0c0;fill-opacity:1;stroke:#000000;stroke-width:0.80000001px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1;marker-start:url(#DotL);marker-mid:url(#DotL);marker-end:url(#DotL)" /><path
+ sodipodi:nodetypes="cc"
+ inkscape:connector-curvature="0"
+ id="path6888-9"
+ d="m 374.96603,1339.988 -24,8"
+ style="fill:none;stroke:#000000;stroke-width:0.80000001px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1;marker-end:url(#Arrow1Mend)" /></g><text
+ xml:space="preserve"
+ style="font-size:12.80000019px;font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;text-align:start;line-height:125%;letter-spacing:0px;word-spacing:0px;writing-mode:lr-tb;text-anchor:start;fill:#000000;fill-opacity:1;stroke:none;font-family:Sans;-inkscape-font-specification:Sans"
+ x="1411.988"
+ y="398.96603"
+ id="text6324-0-3"
+ sodipodi:linespacing="125%"
+ transform="matrix(0,1,1,0,0,0)"><tspan
+ sodipodi:role="line"
+ id="tspan9634"
+ x="1411.988"
+ y="398.96603">C</tspan></text>
+<path
+ style="fill:none;stroke:#000000;stroke-width:0.80000001px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1;marker-end:url(#Arrow1Mend-7)"
+ d="m 390.96603,1491.988 -56,0"
+ id="path9638"
+ inkscape:connector-curvature="0"
+ sodipodi:nodetypes="cc" /><text
+ xml:space="preserve"
+ style="font-size:6.4000001px;font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;text-align:start;line-height:125%;letter-spacing:0px;word-spacing:0px;writing-mode:lr-tb;text-anchor:start;fill:#000000;fill-opacity:1;stroke:none;font-family:Sans;-inkscape-font-specification:Sans"
+ x="1487.988"
+ y="362.96603"
+ id="text10052"
+ sodipodi:linespacing="125%"
+ transform="matrix(0,1,1,0,0,0)"><tspan
+ sodipodi:role="line"
+ id="tspan10054"
+ x="1487.988"
+ y="362.96603">z</tspan></text>
+<text
+ xml:space="preserve"
+ style="font-size:12.80000019px;font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;text-align:start;line-height:125%;letter-spacing:0px;word-spacing:0px;writing-mode:lr-tb;text-anchor:start;fill:#000000;fill-opacity:1;stroke:none;font-family:Sans;-inkscape-font-specification:Sans"
+ x="1507.988"
+ y="398.96603"
+ id="text6324-0-3-9"
+ sodipodi:linespacing="125%"
+ transform="matrix(0,1,1,0,0,0)"><tspan
+ sodipodi:role="line"
+ id="tspan10094"
+ x="1507.988"
+ y="398.96603">D</tspan></text>
+<path
+ style="fill:none;stroke:#000000;stroke-width:1;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-opacity:1;stroke-dasharray:3, 3;stroke-dashoffset:0;marker-start:url(#marker9565)"
+ d="M 390,121.36368 435,76.363678"
+ id="path10096"
+ inkscape:connector-curvature="0"
+ transform="matrix(0,0.8,0.8,0,285.87509,1211.988)" /><path
+ style="fill:none;stroke:#000000;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1;marker-start:url(#marker9565);marker-end:url(#marker9565)"
+ d="m 425,46.363678 20,60.000002"
+ id="path10510"
+ inkscape:connector-curvature="0"
+ transform="matrix(0,0.8,0.8,0,285.87509,1211.988)" /><g
+ id="g8666-2"
+ transform="translate(24,92)"><path
+ sodipodi:nodetypes="ccc"
+ inkscape:connector-curvature="0"
+ id="path5759-6"
+ d="m 326.96603,1235.988 8,24 -24,8"
+ style="fill:none;stroke:#000000;stroke-width:0.80000001px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1;marker-start:url(#Arrow1Mstart);marker-end:url(#Arrow1Mend)" /><path
+ sodipodi:end="5.0360538"
+ sodipodi:start="3.4037817"
+ transform="matrix(0,0.8,0.8,0,41.880104,1195.988)"
+ d="m 61.517651,360.53369 c 2.73936,-10.20752 13.23488,-16.26166 23.442399,-13.5223 0.378769,0.10165 0.754323,0.21492 1.126132,0.33965"
+ sodipodi:ry="19.136335"
+ sodipodi:rx="19.136335"
+ sodipodi:cy="365.49374"
+ sodipodi:cx="80"
+ id="path6322-1"
+ style="fill:none;stroke:#000000;stroke-width:1;stroke-miterlimit:4;stroke-opacity:1;stroke-dasharray:none;marker-start:none"
+ sodipodi:type="arc"
+ sodipodi:open="true" /></g><g
+ id="g8666-2-7"
+ transform="translate(16,208)"><path
+ sodipodi:nodetypes="ccc"
+ inkscape:connector-curvature="0"
+ id="path5759-6-9"
+ d="m 310.96603,1259.988 24,0 -24,8"
+ style="fill:none;stroke:#000000;stroke-width:0.80000001px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1;marker-start:url(#Arrow1Mstart);marker-end:url(#Arrow1Mend)" /><path
+ sodipodi:open="true"
+ sodipodi:end="5.060828"
+ sodipodi:start="4.7003192"
+ transform="matrix(0,0.8,0.8,0,41.880104,1195.988)"
+ d="m 79.769034,346.3588 c 2.305685,-0.0278 4.597418,0.36128 6.764705,1.14857"
+ sodipodi:ry="19.136335"
+ sodipodi:rx="19.136335"
+ sodipodi:cy="365.49374"
+ sodipodi:cx="80"
+ id="path6322-1-9"
+ style="fill:none;stroke:#000000;stroke-width:1;stroke-miterlimit:4;stroke-opacity:1;stroke-dasharray:none;marker-start:none"
+ sodipodi:type="arc" /></g></g></svg>
\ No newline at end of file
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff
