# To help us fund GROMACS development, we humbly ask that you cite
# the research papers on the package. Check out http://www.gromacs.org.
-file(GLOB TOP_LEVEL_FILES ${SOURCE_HTML_DIR}/*.html)
-file(COPY ${TOP_LEVEL_FILES} DESTINATION .)
-file(COPY ${SOURCE_HTML_DIR}/images DESTINATION .)
-file(COPY ${SOURCE_HTML_DIR}/online DESTINATION .)
+if (NOT DEFINED OUTPUT_DIR OR NOT DEFINED SOURCE_HTML_DIR)
+ message(FATAL_ERROR "Required input parameter not set")
+endif()
+
+function(PRE_EXPORT_ACTIONS)
+ file(MAKE_DIRECTORY ${OUTPUT_DIR})
+ file(MAKE_DIRECTORY ${OUTPUT_DIR}/programs)
+ file(COPY ${SOURCE_HTML_DIR}/header.html.in DESTINATION .)
+ file(COPY ${SOURCE_HTML_DIR}/footer.html DESTINATION .)
+endfunction()
+
+function(POST_EXPORT_ACTIONS)
+ # This is generated by gmx help -export html
+ set(HEADER_FILE header.html)
+ set(FOOTER_FILE ${SOURCE_HTML_DIR}/footer.html)
+ file(READ ${HEADER_FILE} HEADER_TEXT)
+ file(READ ${FOOTER_FILE} FOOTER_TEXT)
+ set(_title_re "[Tt][Ii][Tt][Ll][Ee]")
+
+ function(CREATE_HTML_FILE SOURCE_FILE ROOTPATH)
+ file(RELATIVE_PATH _rel_path ${SOURCE_HTML_DIR} ${SOURCE_FILE})
+ file(READ ${SOURCE_FILE} _content)
+ string(REGEX REPLACE "^ *<${_title_re}>(.*)</${_title_re}>\n" "" _content "${_content}")
+ set(TITLE "${CMAKE_MATCH_1}")
+ string(CONFIGURE "${HEADER_TEXT}" _header @ONLY)
+ set(_content "${_header}${_content}${FOOTER_TEXT}")
+ file(WRITE ${OUTPUT_DIR}/${_rel_path} "${_content}")
+ endfunction()
+
+ create_html_file(${SOURCE_HTML_DIR}/online.html "")
+ file(COPY ${SOURCE_HTML_DIR}/images DESTINATION ${OUTPUT_DIR})
+ file(MAKE_DIRECTORY ${OUTPUT_DIR}/online)
+ file(COPY ${SOURCE_HTML_DIR}/online/style.css DESTINATION ${OUTPUT_DIR}/online)
+ file(GLOB _source_files ${SOURCE_HTML_DIR}/online/*.html)
+ foreach(_file ${_source_files})
+ create_html_file(${_file} "../")
+ endforeach()
+endfunction()
+
+if (STEP STREQUAL "PRE")
+ pre_export_actions()
+elseif (STEP STREQUAL "POST")
+ post_export_actions()
+else()
+ message(FATAL_ERROR "Unknown parameter STEP=${STEP}")
+endif()
endif()
if(CAN_BUILD_HTMLHELP)
- file(MAKE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/programs)
- add_custom_target(html-programs
- gmx -quiet help -export html
- WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/programs
- COMMENT "Generating HTML help for programs"
- VERBATIM)
- # TODO: May not work for an in-source build.
+ set(OUTPUT_DIR final)
add_custom_target(html
${CMAKE_COMMAND}
-D SOURCE_HTML_DIR=${CMAKE_CURRENT_SOURCE_DIR}
+ -D OUTPUT_DIR=${OUTPUT_DIR}
+ -D STEP=PRE
+ -P ${CMAKE_CURRENT_SOURCE_DIR}/BuildHtmlHelp.cmake
+ COMMAND gmx -quiet help -export html
+ COMMAND ${CMAKE_COMMAND}
+ -D SOURCE_HTML_DIR=${CMAKE_CURRENT_SOURCE_DIR}
+ -D OUTPUT_DIR=${OUTPUT_DIR}
+ -D STEP=POST
-P ${CMAKE_CURRENT_SOURCE_DIR}/BuildHtmlHelp.cmake
- WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
COMMENT "Generating HTML help"
VERBATIM)
- add_dependencies(html html-programs)
set_directory_properties(PROPERTIES
- ADDITIONAL_MAKE_CLEAN_FILES programs)
+ ADDITIONAL_MAKE_CLEAN_FILES "${OUTPUT_DIR};header.html")
endif()
--- /dev/null
+
+<P>
+<HR>
+<DIV ALIGN=RIGHT><FONT SIZE="-1">
+<A HREF="http://www.gromacs.org">http://www.gromacs.org</A><BR>
+</FONT></DIV>
+</BODY>
+</HTML>
--- /dev/null
+<HTML>
+<HEAD>
+ <TITLE>@TITLE@</TITLE>
+ <LINK rel=stylesheet href="@ROOTPATH@online/style.css" type="text/css">
+</HEAD>
+<BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
+ <TABLE WIDTH="98%%">
+ <TR>
+ <TD WIDTH="116" ROWSPAN="2">
+ <A HREF="http://www.gromacs.org/"><IMG SRC="@ROOTPATH@images/gmxlogo_small.jpg" BORDER=0></A>
+ </TD>
+ <TD ALIGN="LEFT" VALIGN="CENTER" COLSPAN="2">
+ <H2>@TITLE@</H2>
+ </TD>
+ </TR>
+ <TR>
+ <TD>
+ <FONT SIZE="-1"><A HREF="@ROOTPATH@online.html">Main Table of Contents</A></FONT>
+ </TD>
+ <TD ALIGN="RIGHT" VALIGN="BOTTOM">
+ <B>@VERSION@</B>
+ </TD>
+ </TR>
+</TABLE>
+ <HR>
+
-<HTML>
-<HEAD>
-<TITLE>GROMACS 4.6 Online Reference </TITLE>
-</HEAD>
-<LINK rel=stylesheet href="online/style.css" type="text/css">
-<BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
-
-<table WIDTH="98%" NOSAVE NOBORDER >
-<TR><TD WIDTH=400>
-<TABLE WIDTH=400 NOBORDER>
-<TD WIDTH=116>
-<a href="http://www.gromacs.org/">
-<img SRC="images/gmxlogo_small.jpg" BORDER=0 height=133 width=116></a></td>
-<td ALIGN=LEFT VALIGN=TOP WIDTH=280>
-<br><br>
-<h2>
-GROMACS 4.6<br>
-Online Reference</h2>
-</td>
-</TABLE></TD>
-<td ALIGN=RIGHT VALIGN=BOTTOM WIDTH="*" NOSAVE>
-<B>VERSION 4.6<br>
-Sat 19 Jan 2013</B></td>
-</tr>
-</table>
-
-<hr>
-
+<TITLE>GROMACS Online Reference</TITLE>
<TABLE BORDER=0 CELLSPACING=0 CELLPADDING=10>
<TR>
<TD VALIGN=top WIDTH="25%">
</TD>
</TR>
</TABLE>
-<p>
-<HR>
-<div ALIGN=RIGHT><font size="-1">
-<a href="http://www.gromacs.org">http://www.gromacs.org</a><br>
-</font></div>
-</body>
-</html>
<title>cpt file format</title>
-<LINK rel=stylesheet href="style.css" type="text/css">
-<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
-<h2>cpt file format</h2>
-<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
-<TR>
-<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 4.6</B></TR>
-<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
-<TD ALIGN=RIGHT><B>Sat 19 Jan 2013</B></TR></TABLE></CENTER><HR>
<h3>Description</h3>
The cpt file extension stands for portable checkpoint file.
The complete state of the simulation is stored in the checkpoint file,
With domain decomposition also the some decomposition setup information
is stored.
<p>
-See also <a href="mdrun.html">mdrun</a>.
-<hr>
-<div ALIGN=RIGHT>
-<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-</div>
-</body>
+See also <a href="../programs/gmx-mdrun.html">gmx mdrun</a>.
<title>dat file format</title>
-<LINK rel=stylesheet href="style.css" type="text/css">
-<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
-<h2>dat file format</h2>
-<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
-<TR>
-<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 4.6</B></TR>
-<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
-<TD ALIGN=RIGHT><B>Sat 19 Jan 2013</B></TR></TABLE></CENTER><HR>
<H3>Description</H3>
Files with the dat file extension contain generic input or output.
As it is not possible
to categorise all data file formats, GROMACS has a generic file format called
dat of which no format is given.
-<hr>
-<div ALIGN=RIGHT>
-<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-</div>
-</body>
<title>dlg file format</title>
-<LINK rel=stylesheet href="style.css" type="text/css">
-<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
-<h2>dlg file format</h2>
-<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
-<TR>
-<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 4.6</B></TR>
-<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
-<TD ALIGN=RIGHT><B>Sat 19 Jan 2013</B></TR></TABLE></CENTER><HR>
<h3>Description</h3>
-The dlg file format is used as input for the <a href="ngmx.html">ngmx</a>
+The dlg file format is used as input for the
+<a href="../programs/gmx-view.html">gmx view</a>
trajectory viewer. These files are not meant to be altered bu the end user.
<h3>Sample</h3>
<pre>
}
</pre>
-<hr>
-<div ALIGN=RIGHT>
-<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-</div>
-</body>
<title>edi file format</title>
-<LINK rel=stylesheet href="style.css" type="text/css">
-<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
-<h2>edi file format</h2>
-<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
-<TR>
-<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 4.6</B></TR>
-<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
-<TD ALIGN=RIGHT><B>Sat 19 Jan 2013</B></TR></TABLE></CENTER><HR>
<h3>Description</h3>
-Files with the edi file extension contain information for <a href="mdrun.html">
-mdrun</a> to run Molecular Dynamics with Essential Dynamics constraints.
+Files with the edi file extension contain information for
+<a href="../programs/gmx-mdrun.html">gmx mdrun</a>
+to run Molecular Dynamics with Essential Dynamics constraints.
These files can be generated by the program <tt>WEDSAM</tt> which uses
output from the programs in the <tt>ESSDYN</tt> menu of the
<A HREF="http://www.sander.embl-heidelberg.de/whatif/">WHAT IF</A> program.
-</TD> </TR> </TABLE>
-<hr>
-<div ALIGN=RIGHT>
-<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-</div>
-</body>
<title>edo file format</title>
-<LINK rel=stylesheet href="style.css" type="text/css">
-<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
-<h2>edo file format</h2>
-<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
-<TR>
-<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 4.6</B></TR>
-<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
-<TD ALIGN=RIGHT><B>Sat 19 Jan 2013</B></TR></TABLE></CENTER><HR>
<h3>Description</h3>
-Files with the edo file extension are generated by <a href="mdrun.html">
-mdrun</a> if Molecular Dynamics is performed with Essential Dynamics
+Files with the edo file extension are generated by
+<a href="../programs/gmx-mdrun.html">gmx mdrun</a>
+if Molecular Dynamics is performed with Essential Dynamics
constraints. Depending on the parameters set in the <a href="edi.html">
edi</a> file, edo files may contain projections of positions,
velocities and forces onto selected eigenvectors during the run as well
as RMSD values, or information about specific types of constraints.
Specific results can be extracted from the edo files with standard unix
utilities like <tt>awk</tt>.
-<hr>
-<div ALIGN=RIGHT>
-<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-</div>
-</body>
<title>ene file format</title>
-<LINK rel=stylesheet href="style.css" type="text/css">
-<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
-<h2>edr file format</h2>
-<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
-<TR>
-<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 4.6</B></TR>
-<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
-<TD ALIGN=RIGHT><B>Sat 19 Jan 2013</B></TR></TABLE></CENTER><HR>
<h3>Description</h3>
The edr file extension stands for portable energy file.
The energies are stored using the xdr protocol.
<p>
-See also <a href="g_energy.html">g_energy</a>.
-<hr>
-<div ALIGN=RIGHT>
-<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-</div>
-</body>
+See also <a href="../programs/gmx-energy.html">gmx energy</a>.
<title>ene file format</title>
-<LINK rel=stylesheet href="style.css" type="text/css">
-<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
-<h2>ene file format</h2>
-<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
-<TR>
-<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 4.6</B></TR>
-<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
-<TD ALIGN=RIGHT><B>Sat 19 Jan 2013</B></TR></TABLE></CENTER><HR>
<h3>Description</h3>
The ene file extension stands for binary energy file. It holds the
-energies as generated during your <a href="mdrun.html">mdrun</a>.
+energies as generated during your
+<a href="../programs/gmx-mdrun.html">gmx mdrun</a>.
<br>
The file can be transformed to a portable energy file (portable
accross hardware platforms), the
-<a href="edr.html">.edr</a> file using the program <a href="eneconv.html">
-eneconv</a>.
+<a href="edr.html">.edr</a> file using the program
+<a href="../programs/gmx-eneconv.html">gmx eneconv</a>.
<p>
-See also <a href="g_energy.html">g_energy</a>.
-<hr>
-<div ALIGN=RIGHT>
-<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-</div>
-</body>
+See also <a href="../programs/gmx-energy.html">gmx energy</a>.
<title>eps file format</title>
-<LINK rel=stylesheet href="style.css" type="text/css">
-<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
-<h2>eps file format</h2>
-<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
-<TR>
-<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 4.6</B></TR>
-<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
-<TD ALIGN=RIGHT><B>Sat 19 Jan 2013</B></TR></TABLE></CENTER><HR>
<H3>Description</H3>
The eps file format is not a special GROMACS format, but just a
variant of the standard PostScript(tm). A sample eps file as
-generated by the <a href="xpm2ps.html">xpm2ps</a> program is
+generated by the <a href="../programs/gmx-xpm2ps.html">gmx xpm2ps</a> program is
included below. It shows the secondary structure of a peptide as a function
of time.
<p>
<img src="../images/plotje.gif" alt="hallo">
-<hr>
-<div ALIGN=RIGHT>
-<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-
-</div>
-</body>
-<HTML>
-<HEAD>
<TITLE>File formats</TITLE>
-<LINK rel=stylesheet href="style.css" type="text/css">
-<BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
-<TABLE WIDTH="98%" NOBORDER >
-<TR><TD WIDTH=400>
-<TABLE WIDTH=400 NOBORDER>
-<TD WIDTH=116>
-<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
-<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>GROMACS<br>File Formats</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
-Sat 19 Jan 2013</B></td></tr></TABLE>
-<HR>
<dl>
<dt><h3>Parameter files</h3>
<dl compact>
<a href="mdp.html">mdp</a>
-<dd>run parameters, input for <a href="grompp.html">grompp</a> and
-<a href="tpbconv.html">tpbconv</a>
+<dd>run parameters, input for
+<a href="../programs/gmx-grompp.html">gmx grompp</a> and
+<a href="../programs/tpbconv.html">gmx tpbconv</a>
<dt><a href="m2p.html">m2p</a>
-<dd>input for <a href="xpm2ps.html">xpm2ps</a>
+<dd>input for <a href="../programs/xpm2ps.html">gmx xpm2ps</a>
</dl>
<br><dt><h3>Structure files</h3>
<dd><dl compact>
<dt><a href="dat.html">dat</a> <dd>generic, preferred for input
<dt><a href="edi.html">edi</a>
-<dd>essential dynamics constraints input for <a href="mdrun.html">mdrun</a>
+<dd>essential dynamics constraints input for
+<a href="../programs/gmx-mdrun.html">gmx mdrun</a>
<dt><a href="edo.html">edo</a>
-<dd>essential dynamics constraints output for <a href="mdrun.html">mdrun</a>
+<dd>essential dynamics constraints output for
+<a href="../programs/gmx-mdrun.html">gmx mdrun</a>
<dt><a href="eps.html">eps</a> <dd>Encapsulated Postscript
<dt><a href="log.html">log</a> <dd>log file
-<dt><a href="map.html">map</a> <dd>colormap input for <a href="do_dssp.html">do_dssp</a>
+<dt><a href="map.html">map</a> <dd>colormap input for
+<a href="../programs/gmx-do_dssp.html">gmx do_dssp</a>
<dt><a href="mtx.html">mtx</a> <dd>binary matrix data
<dt><a href="out.html">out</a> <dd>generic, preferred for output
<dt><a href="tex.html">tex</a> <dd>LaTeX input
-<dt><a href="xpm.html">xpm</a> <dd>ascii matrix data, use <a href="xpm2ps.html">xpm2ps</A> to convert to <a href="eps.html">eps</a>
+<dt><a href="xpm.html">xpm</a> <dd>ascii matrix data, use
+<a href="../programs/gmx-xpm2ps.html">gmx xpm2ps</A> to convert to <a href="eps.html">eps</a>
<dt><a href="xvg.html">xvg</a> <dd>xvgr input
</dl>
</dl>
-<hr>
-<div ALIGN=RIGHT>
-<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-</div>
-
-</BODY>
-<HTML>
-<HEAD>
<TITLE>Flow Chart</TITLE>
-<LINK rel=stylesheet href="style.css" type="text/css">
-<BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
-<TABLE WIDTH="98%" NOBORDER >
-<TR><TD WIDTH=400>
-<TABLE WIDTH=400 NOBORDER>
-<TD WIDTH=116>
-<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
-<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>GROMACS<br>Flow chart</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
-Sat 19 Jan 2013</B></td></tr></TABLE>
-<HR>
<p>This is a flow chart of a typical GROMACS MD run of a protein
in a box of water.
A more detailed example is available in the
<A HREF="getting_started.html">Getting Started</A>
section. Several steps of energy minimization may be necessary,
-these consist of cycles: grompp -> mdrun.
+these consist of cycles: grompp -> mdrun.
<p>
<CENTER>
</TABLE>
</CENTER>
-
-<br>
-<hr>
-<div ALIGN=RIGHT>
-<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-
-</div>
-
-</BODY>
-
<title>Gromos87 trajectory file format</title>
-<LINK rel=stylesheet href="style.css" type="text/css">
-<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
-<h2>g87 file format</h2>
-<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
-<TR>
-<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 4.6</B></TR>
-<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
-<TD ALIGN=RIGHT><B>Sat 19 Jan 2013</B></TR></TABLE></CENTER><HR>
+<h3>Description</h3>
This is a simple ASCII format:<br>
<pre>
TITLE
The number of atoms is <b>not</b> stored, neither is there any indication
of whether a box is present. The box is stored only for constant pressure
simulations. So, you simply have to remember this stuff.
-<hr>
-<div ALIGN=RIGHT>
-<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-</div>
-</body>
<title>g96 file format</title>
-<LINK rel=stylesheet href="style.css" type="text/css">
-<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
-<h2>g96 file format</h2>
-<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
-<TR>
-<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 4.6</B></TR>
-<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
-<TD ALIGN=RIGHT><B>Sat 19 Jan 2013</B></TR></TABLE></CENTER><HR>
-
+<h3>Description</h3>
<p>A file with the g96 extension can be a GROMOS-96 initial/final
configuration file or a coordinate trajectory file or a combination of both.
The file is fixed format, all floats are written as 15.9 (files can get huge).
See the GROMOS-96 manual for a complete description of the blocks.
<p>
Note that all GROMACS programs can read compressed or g-zipped files.
-<hr>
-<div ALIGN=RIGHT>
-<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-
-</div>
-
-</body>
-
-<HTML>
-<HEAD>
<TITLE>Getting started</TITLE>
-<LINK rel=stylesheet href="style.css" type="text/css">
-<BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
-<TABLE WIDTH="98%" NOBORDER >
-<TR><TD WIDTH=400>
-<TABLE WIDTH=400 NOBORDER>
-<TD WIDTH=116>
-<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
-<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>Getting started</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.6<br>
-Sat 19 Jan 2013</B></td></tr></TABLE>
-<HR>
<H3>Contents</H3>
<ul>
</dl>
</blockquote>
-
-<br>
-<hr>
-<div ALIGN=RIGHT>
-<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-
-</div>
-</BODY>
-</HTML>
<title>gro file format</title>
-<LINK rel=stylesheet href="style.css" type="text/css">
-<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
-<h2>gro file format</h2>
-<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
-<TR>
-<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 4.6</B></TR>
-<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
-<TD ALIGN=RIGHT><B>Sat 19 Jan 2013</B></TR></TABLE></CENTER><HR>
-
+<h3>Description</h3>
<p>Files with the gro file extension contain a molecular structure in
Gromos87 format. gro files can be used as trajectory by simply
concatenating files. An attempt will be made to read a time value from
Note that this is the format for writing, as in the above example
fields may be written without spaces, and therefore can not be read
with the same format statement in C.
-<hr>
-<div ALIGN=RIGHT>
-<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-
-</div>
-</body>
<title>itp file format</title>
-<LINK rel=stylesheet href="style.css" type="text/css">
-<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
-<h2>itp file format</h2>
-<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
-<TR>
-<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 4.6</B></TR>
-<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
-<TD ALIGN=RIGHT><B>Sat 19 Jan 2013</B></TR></TABLE></CENTER><HR>
<h3>Description</h3>
The itp file extension stands for include toplogy. These files are included in topology files ( with the <a href="top.html"><tt>top</tt></a> extension )
-<hr>
-<div ALIGN=RIGHT>
-<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-</div>
-</body>
<title>log file format</title>
-<LINK rel=stylesheet href="style.css" type="text/css">
-<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
-<h2>log file format</h2>
-<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
-<TR>
-<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 4.6</B></TR>
-<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
-<TD ALIGN=RIGHT><B>Sat 19 Jan 2013</B></TR></TABLE></CENTER><HR>
<h3>Description</h3>
Logfiles are generated by some GROMACS programs and are usually in
human-readable format. Use <tt>more logfile</tt>.
-<hr>
-<div ALIGN=RIGHT>
-<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-
-</div>
-</body>
<title>m2p file format</title>
-<LINK rel=stylesheet href="style.css" type="text/css">
-<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
-<h2>m2p file format</h2>
-<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
-<TR>
-<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 4.6</B></TR>
-<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
-<TD ALIGN=RIGHT><B>Sat 19 Jan 2013</B></TR></TABLE></CENTER><HR>
<h3>Description</h3>
-The m2p file format contains input options for the
-<a href="xpm2ps.html">xpm2ps</a> program. All of these options
+The m2p file format contains input options for the
+<a href="../programs/gmx-xpm2ps.html">gmx xpm2ps</a> program. All of these options
are very easy to comprehend when you look at the PosScript(tm) output
-from <a href="xpm2ps.html">xpm2ps</a>.
+from <a href="../programs/gmx-xpm2ps.html">gmx xpm2ps</a>.
<pre>
; Command line options of xpm2ps override the parameters in this file
black&white = no ; Obsolete
y-tickfontsize = 10
y-tickfont = Helvetica
</pre>
-<hr>
-<div ALIGN=RIGHT>
-<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-</div>
-</body>
<title>map file format</title>
-<LINK rel=stylesheet href="style.css" type="text/css">
-<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
-<h2>map file format</h2>
-<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
-<TR>
-<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 4.6</B></TR>
-<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
-<TD ALIGN=RIGHT><B>Sat 19 Jan 2013</B></TR></TABLE></CENTER><HR>
<H3>Description</H3>
This file maps matrix data to RGB values which is used by the
-<a href="
do_dssp.html">do_dssp</a> program.<p>
+<a href="
../programs/gmx-do_dssp.html">gmx do_dssp</a> program.<p>
The format of this file is as follow: first line number of elements
in the colormap. Then for each line: The first character is
a code for the secondary structure type.
G 3-Helix 1.0 0.0 1.0
I 5-Helix 1.0 0.6 0.0
</pre>
-<hr>
-<div ALIGN=RIGHT>
-<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-</div>
-</body>
-<HTML>
<title>mdp file format</title>
-<LINK rel=stylesheet href="style.css" type="text/css">
-<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
-<h2>mdp file format</h2>
-<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
-<TR>
-<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 4.6</B></TR>
-<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
-<TD ALIGN=RIGHT><B>Sat 19 Jan 2013</B></TR></TABLE></CENTER><HR>
<P> Follow <a href="mdp_opt.html">this link</a> for a detailed description of the options</a>. </P>
<P> Below is a sample mdp file.
userreal3 = 0
userreal4 = 0
</pre>
-
-<hr>
-<div ALIGN=RIGHT>
-<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-</div>
-</body>
-<HTML>
-<HEAD>
<TITLE>mdp options</TITLE>
-<LINK rel=stylesheet href="style.css" type="text/css">
-<BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
-<TABLE WIDTH="98%" NOBORDER >
-<TR><TD WIDTH=400>
-<TABLE WIDTH=400 NOBORDER>
-<TD WIDTH=116>
-<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
-<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>mdp options</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p> </p><B>VERSION 4.6.4</B></td></tr></TABLE>
-<HR>
-
<!--
PLEASE BE VERY CAREFUL WHEN EDITING THIS FILE: IT MUST BE
<A HREF="#expanded">wl-ratio</A><br>
<A HREF="#expanded">wl-scale</A><br>
</multicol>
-
-<hr>
-<div ALIGN=RIGHT>
-<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-
-</div>
-</BODY>
-</HTML>
-
<title>mtx file format</title>
-<LINK rel=stylesheet href="style.css" type="text/css">
-<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
-<h2>mtx file format</h2>
-<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
-<TR>
-<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 4.6</B></TR>
-<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
-<TD ALIGN=RIGHT><B>Sat 19 Jan 2013</B></TR></TABLE></CENTER><HR>
<H3>Description</H3>
Files with the mtx file extension contain a matrix.
The file format is identical to the <a href="trj.html">trj</a> format.
Currently this file format is only used for hessian matrices,
-which are produced with <a href="mdrun.html">mdrun</a> and read by
-<a href="g_nmeig.html">g_nmeig</a>.
-<hr>
-<div ALIGN=RIGHT>
-<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-
-</div>
-</body>
+which are produced with <a href="../programs/gmx-mdrun.html">gmx mdrun</a> and read by
+<a href="../programs/gmx-nmeig.html">gmx nmeig</a>.
<title>ndx file format</title>
-<LINK rel=stylesheet href="style.css" type="text/css">
-<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
-<h2>ndx file format</h2>
-<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
-<TR>
-<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 4.6</B></TR>
-<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
-<TD ALIGN=RIGHT><B>Sat 19 Jan 2013</B></TR></TABLE></CENTER><HR>
<H3>Description</H3>
The GROMACS index file (usually called index.ndx) contains some
user definable sets of atoms. The file can be read by
-most analysis programs, by the graphics program (<a href=ngmx.html>ngmx</a>)
-and by the preprocessor (<a href=grompp.html>grompp</a>).
+most analysis programs, by the graphics program
+(<a href="../programs/gmx-view.html">gmx view</a>)
+and by the preprocessor (<a href="../programs/gmx-grompp.html">gmx grompp</a>).
Most of these programs create default index groups when no index
file is supplied, so you only need to make an index file when you need special
groups.
<b>Oxygen</b> has 3 elements.
The second group <b>Hydrogen</b> has 6 elements.
<p>
-An index file generation tool is available: <a href=make_ndx.html>make_ndx</a>.
-<hr>
-<div ALIGN=RIGHT>
-<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-</div>
-</body>
+An index file generation tool is available:
+<a href="../programs/gmx-make_ndx.html">gmx make_ndx</a>.
<TITLE>Options</TITLE>
-<BODY>
-<H2>Options</H2>
-<B>VERSION 2.0</B><BR>
-<P>
<UL>
<LI>
Optional files are not used unless the option is set, in contrast to
the run input or structure file, but only if the trajectory consists
of the first n atoms of the run input or structure file.
</UL>
-</BODY>
<title>out file format</title>
-<LINK rel=stylesheet href="style.css" type="text/css">
-<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
-<h2>out file format</h2>
-<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
-<TR>
-<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 4.6</B></TR>
-<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
-<TD ALIGN=RIGHT><B>Sat 19 Jan 2013</B></TR></TABLE></CENTER><HR>
<H3>Description</H3>
Files with the out file extension contain generic output. As it is not possible
to categorise all data file formats, GROMACS has a generic file format called
out of which no format is given.
-<hr>
-<div ALIGN=RIGHT>
-<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-
-</div>
-</body>
<title>pdb file format</title>
-<LINK rel=stylesheet href="style.css" type="text/css">
-<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
-<h2>pdb file format</h2>
-<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
-<TR>
-<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 4.6</B></TR>
-<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
-<TD ALIGN=RIGHT><B>Sat 19 Jan 2013</B></TR></TABLE></CENTER><HR>
<H3>Description</H3>
Files with the <a href="pdb.html">.pdb</a> extension are molecular
...
...
</PRE>
-
-<p>
-<a href="../tutor/speptide/speptide.pdb.txt">speptide.pdb</a>:
-Protein structure file of Ribonuclease A speptide in protein data
-bank file format.
-
-<p>
-Links to descriptions of the pdb format
-can be found on the <A HREF="../links.html">Links page</A>.
-
-<p>
-<hr>
-<div ALIGN=RIGHT>
-<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-
-</div>
-
-</body>
<title>rtp file format</title>
-<LINK rel=stylesheet href="style.css" type="text/css">
-<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
-<h2>rtp file format</h2>
-<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
-<TR>
-<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 4.6</B></TR>
-<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
-<TD ALIGN=RIGHT><B>Sat 19 Jan 2013</B></TR></TABLE></CENTER><HR>
<H3>Description</H3>
The rtp file extension stands for residue toplogy.
-Such a file is needed by <a href="pdb2gmx.html">pdb2gmx</a>
+Such a file is needed by <a href="../programs/gmx-pdb2gmx.html">gmx pdb2gmx</a>
to make a GROMACS topology for a protein contained in a <tt>.pdb</tt>
file. The file contains the default interaction type for the 4 bonded
interactions and residue entries, which consist of atoms and
the string is copied to the <a href="top.html"><tt>.top</tt></a> file,
this is used for the GROMOS96 forcefield.
<p>
-<a href="pdb2gmx.html">pdb2gmx</a> automatically generates all angles,
+<a href="../programs/gmx-pdb2gmx.html">gmx pdb2gmx</a>
+automatically generates all angles,
this means that the <tt>[angles]</tt> field is only
useful for overriding <a href="itp.html"><tt>.itp</tt></a> parameters.
<p>
-<a href="pdb2gmx.html">pdb2gmx</a> automatically generates one proper
+<a href="../programs/gmx-pdb2gmx.html">gmx pdb2gmx</a>
+automatically generates one proper
dihedral for every rotatable bond, preferably on heavy atoms.
When the <tt>[dihedrals]</tt> field is used, no other dihedrals will
be generated for the bonds corresponding to the specified dihedrals.
It is possible to put more than one dihedral on a rotatable bond.
<p>
-<a href="pdb2gmx.html">pdb2gmx</a> sets the number exclusions to 3, which
+<a href="../programs/gmx-pdb2gmx.html">gmx pdb2gmx</a>
+sets the number exclusions to 3, which
means that interactions between atoms connected by at most 3 bonds are
excluded. Pair interactions are generated for all pairs of atoms which are
seperated by 3 bonds (except pairs of hydrogens).
[ atoms ]
ZN ZN 2.000 0
</PRE>
-<hr>
-<div ALIGN=RIGHT>
-<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-
-</div>
-</body>
<title>tex file format</title>
-<LINK rel=stylesheet href="style.css" type="text/css">
-<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
-<h2>tex file format</h2>
-<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
-<TR>
-<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 4.6</B></TR>
-<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
-<TD ALIGN=RIGHT><B>Sat 19 Jan 2013</B></TR></TABLE></CENTER><HR>
<H3>Description</H3>
We use <b>LaTeX</b> for <i>document</i> processing.
Although the input is not so
<li> It makes anything from letters to a thesis
<li> Much more...
</ul>
-<hr>
-<div ALIGN=RIGHT>
-<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-
-</div>
-</body>
<title>top file format</title>
-<LINK rel=stylesheet href="style.css" type="text/css">
-<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
-<h2>top file format</h2>
-<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
-<TR>
-<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 4.6</B></TR>
-<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
-<TD ALIGN=RIGHT><B>Sat 19 Jan 2013</B></TR></TABLE></CENTER><HR>
<H3>Description</H3>
The top file extension stands for topology. It is an ascii file which is
-read by <a href="grompp.html">grompp</a> which processes it
-and creates a binary topology (<a href="tpb.html">tpb-file</a>).<br>
+read by <a href="../programs/gmx-grompp.html">gmx grompp</a> which processes it
+and creates a binary topology (<a href="tpb.html">.tpb file</a>).<br>
A sample file is included below:
<pre>
;
Urea 1
SOL 1000
</pre>
-<hr>
-<div ALIGN=RIGHT>
-<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-</div>
-</body>
<title>tpa file format</title>
-<LINK rel=stylesheet href="style.css" type="text/css">
-<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
-<h2>tpa file format</h2>
-<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
-<TR>
-<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 4.6</B></TR>
-<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
-<TD ALIGN=RIGHT><B>Sat 19 Jan 2013</B></TR></TABLE></CENTER><HR>
<H3>Description</H3>
The tpa file extension stands for binary run input file. This file contains
the starting structure of your simulation, The molecular topology and
all the simulation data. Because this file is in binary format it
cannot be read with a normal editor. To read a binary run input file type:
<PRE>
-% <a href="gmxdump.html">gmxdump</a> -s topol.tpa
+% <a href="../programs/gmx-dump.html">gmx dump</a> -s topol.tpa
</PRE>
or if you're not such a fast reader:
<PRE>
<p>
You can also compare two tpa files using:
<pre>
-% <a href="gmxcheck.html">gmxcheck</a> -s1 top1 -s2 top2 | more
+% <a href="../programs/gmx-check.html">gmx check</a> -s1 top1 -s2 top2 | more
</pre>
-<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
-<TR>
-<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 4.6</B></TR>
-<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
-<TD ALIGN=RIGHT><B>Sat 19 Jan 2013</B></TR></TABLE></CENTER><HR>
-</body>
<title>tpb file format</title>
-<LINK rel=stylesheet href="style.css" type="text/css">
-<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
-<h2>tpb file format</h2>
-<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
-<TR>
-<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 4.6</B></TR>
-<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
-<TD ALIGN=RIGHT><B>Sat 19 Jan 2013</B></TR></TABLE></CENTER><HR>
<h3>Description</h3>
The tpb file extension stands for binary run input file. This file contains
the starting structure of your simulation, The molecular topology and
all the simulation data. Because this file is in binary format it
cannot be read with a normal editor. To read a binary run input file type:
<PRE>
-% <a href="gmxdump.html">gmxdump</a> -s topol.tpb
+% <a href="../programs/gmx-dump.html">gmx dump</a> -s topol.tpb
</PRE>
or if you're not such a fast reader:
<PRE>
<p>
You can also compare two tpb files using:
<pre>
-% <a href="gmxcheck.html">gmxcheck</a> -s1 top1 -s2 top2 | more
+% <a href="../programs/gmx-check.html">gmx check</a> -s1 top1 -s2 top2 | more
</pre>
-<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
-<TR>
-<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 4.6</B></TR>
-<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
-<TD ALIGN=RIGHT><B>Sat 19 Jan 2013</B></TR></TABLE></CENTER><HR>
-</body>
<title>tpr file format</title>
-<LINK rel=stylesheet href="style.css" type="text/css">
-<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
-<h2>tpr file format</h2>
-<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
-<TR>
-<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 4.6</B></TR>
-<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
-<TD ALIGN=RIGHT><B>Sat 19 Jan 2013</B></TR></TABLE></CENTER><HR>
<h3>Description</h3>
The tpr file extension stands for portable binary run input file. This file
contains the starting structure of your simulation, the molecular topology
cannot be read with a normal editor. To read a portable binary run input
file type:
<PRE>
-% <a href="gmxdump.html">gmxdump</a> -s topol.tpr
+% <a href="../programs/gmx-dump.html">gmx dump</a> -s topol.tpr
</PRE>
or if you're not such a fast reader:
<PRE>
<p>
You can also compare two tpr files using:
<pre>
-<a href="gmxcheck.html">gmxcheck</a> -s1 top1 -s2 top2 | more
+% <a href="../programs/gmx-check.html">gmx check</a> -s1 top1 -s2 top2 | more
</pre>
-<hr>
-<div ALIGN=RIGHT>
-<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-</div>
-</body>
<title>trj file format</title>
-<LINK rel=stylesheet href="style.css" type="text/css">
-<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
-<h2>trj file format</h2>
-<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
-<TR>
-<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 4.6</B></TR>
-<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
-<TD ALIGN=RIGHT><B>Sat 19 Jan 2013</B></TR></TABLE></CENTER><HR>
<h3>Description</h3>
Files with the trj file extension contain the trajectory of a simulation.
In this file all the coordinates, velocities, forces and energies are
printed as you told GROMACS in your mdp file. This file is in binary
-format an can be read with <a href=gmxdump.html>gmxdump</a>.
+format an can be read with <a href="../programs/gmx-dump.html">gmx dump</a>.
<PRE>
-% <a href="gmxdump.html">gmxdump</a> -f traj.trj
+% <a href="../programs/gmx-dump.html">gmx dump</a> -f traj.trj
</PRE>
or if you're not such a fast reader:
<PRE>
You can also get a quick look in the contents of the file (number of
frames etc.) using:
<PRE>
-% <a href="gmxcheck.html">gmxcheck</a> -f traj.trj
+% <a href="../programs/gmx-check.html">gmx check</a> -f traj.trj
</PRE>
-<hr>
-<div ALIGN=RIGHT>
-<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-
-</div>
-</body>
<title>trr file format</title>
-<LINK rel=stylesheet href="style.css" type="text/css">
-<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
-<h2>trr file format</h2>
-<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
-<TR>
-<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 4.6</B></TR>
-<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
-<TD ALIGN=RIGHT><B>Sat 19 Jan 2013</B></TR></TABLE></CENTER><HR>
<h3>Description</h3>
Files with the trr file extension contain the trajectory of a simulation.
In this file all the coordinates, velocities, forces and energies are
printed as you told GROMACS in your mdp file. This file is in portable binary
-format an can be read with <a href=gmxdump.html>gmxdump</a>.
+format an can be read with <a href="../programs/gmx-dump.html">gmx dump</a>.
<PRE>
-% <a href="gmxdump.html">gmxdump</a> -f traj.trr
+% <a href="../programs/gmx-dump.html">gmx dump</a> -f traj.trr
</PRE>
or if you're not such a fast reader:
<PRE>
You can also get a quick look in the contents of the file (number of
frames etc.) using:
<PRE>
-% <a href="gmxcheck.html">gmxcheck</a> -f traj.trr
+% <a href="../programs/gmx-check.html">gmx check</a> -f traj.trr
</PRE>
-<hr>
-<div ALIGN=RIGHT>
-<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-
-</div>
-</body>
<title>xpm file format</title>
-<LINK rel=stylesheet href="style.css" type="text/css">
-<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
-<h2>xpm file format</h2>
-<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
-<TR>
-<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 4.6</B></TR>
-<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
-<TD ALIGN=RIGHT><B>Sat 19 Jan 2013</B></TR></TABLE></CENTER><HR>
<H3>Description</H3>
The GROMACS xpm file format is compatible with the XPixMap format
and is used for storing matrix data.
In addition to the XPixMap format, GROMACS xpm files may contain
extra fields. The information in these fields is used when converting
an xpm file to EPS with
-<A HREF="xpm2ps.html">xpm2ps</a>.
+<A HREF="../programs/gmx-xpm2ps.html">gmx xpm2ps</a>.
The optional extra field are:
<ul>
<li>
"DACCDDDDDDEEE",
"ADEEEEEEEFFFF"
</pre>
-<hr>
-<div ALIGN=RIGHT>
-<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-</div>
-</body>
<title>xtc file format</title>
-<LINK rel=stylesheet href="style.css" type="text/css">
-<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
-<h2>xtc file format</h2>
-<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
-<TR>
-<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 4.6</B></TR>
-<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
-<TD ALIGN=RIGHT><B>Sat 19 Jan 2013</B></TR></TABLE></CENTER><HR>
<H3>Description</H3>
The xtc format is a <b>portable</b> format for trajectories.
It uses the <i>xdr</i> routines for writing and reading
on your linker command line.
The source for this test can be found in file
<tt>$(GMXHOME)/src/gmxlib/testxtcf.f</ff>.
-<hr>
-<div ALIGN=RIGHT>
-<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-</div>
-</body>
-<title>xvgr</title>
-<LINK rel=stylesheet href="style.css" type="text/css">
-<BODY text="#000000" bgcolor="#FFFFFF" link="#0000EF" vlink="#650065" alink="#FF0000">
-<h2>GRACE/XMGR, The ultimate plotting program</h2>
-<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
-<TR>
-<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 4.6</B></TR>
-<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
-<TD ALIGN=RIGHT><B>Sat 19 Jan 2013</B></TR></TABLE></CENTER><HR>
+<title>xvgr file format</title>
<H3>Description</H3>
Almost all output from GROMACS analysis tools is ready as input for
Grace, formerly known as Xmgr. We use Grace, because it is very flexible, and it is also
<p>
A sample Grace session with GROMACS data is shown below.<br><br>
<img src="../images/xvgr.gif" alt="xvgr window"> <br>
-<p>
-<hr>
-<div ALIGN=RIGHT>
-<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-</div>
-</body>
virtual void finishModuleGroupExport();
private:
+ void setupHeaderAndFooter();
+
void writeHtmlHeader(File *file, const std::string &title) const;
void writeHtmlFooter(File *file) const;
boost::scoped_ptr<File> indexFile_;
HelpLinks links_;
+ std::string header_;
+ std::string footer_;
};
HelpExportHtml::HelpExportHtml(const CommandLineModuleMap &modules)
links_.addLink(line, "../online/" + line, line);
}
}
+ setupHeaderAndFooter();
+}
+
+void HelpExportHtml::setupHeaderAndFooter()
+{
+ header_ = gmx::File::readToString("header.html.in");
+ header_ = replaceAll(header_, "@VERSION@", GromacsVersion());
+ gmx::File::writeFileFromString("header.html", header_);
+ header_ = replaceAll(header_, "@ROOTPATH@", "../");
+ footer_ = gmx::File::readToString("footer.html");
}
void HelpExportHtml::startModuleExport()
{
- indexFile_.reset(new File("byname.html", "w"));
+ indexFile_.reset(new File("final/programs/byname.html", "w"));
writeHtmlHeader(indexFile_.get(), "GROMACS Programs by Name");
indexFile_->writeLine("<H3>GROMACS Programs Alphabetically</H3>");
}
const std::string &tag,
const std::string &displayName)
{
- File file(tag + ".html", "w");
+ File file("final/programs/" + tag + ".html", "w");
writeHtmlHeader(&file, displayName);
CommandLineHelpContext context(&file, eHelpOutputFormat_Html, &links_);
void HelpExportHtml::startModuleGroupExport()
{
- indexFile_.reset(new File("bytopic.html", "w"));
+ indexFile_.reset(new File("final/programs/bytopic.html", "w"));
writeHtmlHeader(indexFile_.get(), "GROMACS Programs by Topic");
indexFile_->writeLine("<H3>GROMACS Programs by Topic</H3>");
}
void HelpExportHtml::writeHtmlHeader(File *file, const std::string &title) const
{
- file->writeLine("<HTML>");
- file->writeLine("<HEAD>");
- file->writeLine(formatString("<TITLE>%s</TITLE>", title.c_str()));
- file->writeLine("<LINK rel=stylesheet href=\"../online/style.css\" type=\"text/css\">");
- file->writeLine("<BODY text=\"#000000\" bgcolor=\"#FFFFFF\" link=\"#0000FF\" vlink=\"#990000\" alink=\"#FF0000\">");
- file->writeLine("<TABLE WIDTH=\"98%%\" NOBORDER><TR>");
- file->writeLine("<TD WIDTH=400><TABLE WIDTH=400 NOBORDER>");
- file->writeLine("<TD WIDTH=116>");
- file->writeLine("<A HREF=\"http://www.gromacs.org/\">"
- "<IMG SRC=\"../images/gmxlogo_small.jpg\" BORDER=0>"
- "</A>");
- file->writeLine("</TD>");
- file->writeLine(formatString("<TD ALIGN=LEFT VALIGN=TOP WIDTH=280>"
- "<BR><H2>%s</H2>", title.c_str()));
- file->writeLine("<FONT SIZE=-1><A HREF=\"../online.html\">Main Table of Contents</A></FONT>");
- file->writeLine("</TD>");
- file->writeLine("</TABLE></TD>");
- file->writeLine("<TD WIDTH=\"*\" ALIGN=RIGHT VALIGN=BOTTOM>");
- file->writeLine(formatString("<P><B>%s</B>", GromacsVersion()));
- file->writeLine("</TD>");
- file->writeLine("</TR></TABLE>");
- file->writeLine("<HR>");
+ file->writeLine(replaceAll(header_, "@TITLE@", title));
}
void HelpExportHtml::writeHtmlFooter(File *file) const
{
- file->writeLine("<P>");
- file->writeLine("<HR>");
- file->writeLine("<DIV ALIGN=RIGHT><FONT SIZE=\"-1\">");
- file->writeLine("<A HREF=\"http://www.gromacs.org\">http://www.gromacs.org</A><BR>");
- file->writeLine("</FONT></DIV>");
- file->writeLine("</BODY>");
- file->writeLine("</HTML>");
+ file->writeLine(footer_);
}
} // namespace
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff