From: Teemu Murtola <teemu.murtola@gmail.com>
Date: Mon, 15 Jun 2015 15:28:33 +0000 (+0300)
Subject: Fix broken links from the old flow chart
X-Git-Url: http://biod.pnpi.spb.ru/gitweb/?a=commitdiff_plain;h=4881443ce542ebb484a46398e45639a9d011ddb2;p=alexxy%2Fgromacs.git

Fix broken links from the old flow chart

The program help pages got moved from programs/ to onlinehelp/, but
these explicit links were forgotten.

Change-Id: Ia37f4b20d37f40f727835bca71d9b85f3260502c
---

diff --git a/docs/user-guide/flow.rst b/docs/user-guide/flow.rst
index 52d1f817d3..9d81f3618f 100644
--- a/docs/user-guide/flow.rst
+++ b/docs/user-guide/flow.rst
@@ -7,9 +7,6 @@ A more detailed example is available in :doc:`getting-started`.
 Several steps of energy minimization may be necessary,
 these consist of cycles: :ref:`gmx grompp` -> :ref:`gmx mdrun`.
 
-.. URL="file-formats.html#pdb"
-.. ../programs/gmx-pdb2gmx.html
-
 .. digraph:: flowchart
 
    node [ shape=box, width=1.5 ]
@@ -24,7 +21,7 @@ these consist of cycles: :ref:`gmx grompp` -> :ref:`gmx mdrun`.
    pdb2gmx [
      label="Generate a GROMACS topology\ngmx pdb2gmx"
      tooltip="Convert PDB file to GROMACS coordinate file and topology"
-     URL="../programs/gmx-pdb2gmx.html"
+     URL="../onlinehelp/gmx-pdb2gmx.html"
      width=3
      group=main
    ]
@@ -34,7 +31,7 @@ these consist of cycles: :ref:`gmx grompp` -> :ref:`gmx mdrun`.
    editconf [
      label="Enlarge the box\ngmx editconf"
      tooltip="Adjust box size and placement of molecule"
-     URL="../programs/gmx-editconf.html"
+     URL="../onlinehelp/gmx-editconf.html"
    ]
 
    pdb2gmx -> editconf [
@@ -46,7 +43,7 @@ these consist of cycles: :ref:`gmx grompp` -> :ref:`gmx mdrun`.
    solvate [
      label="Solvate protein\ngmx solvate"
      tooltip="Fill box with water (solvate molecule)"
-     URL="../programs/gmx-solvate.html"
+     URL="../onlinehelp/gmx-solvate.html"
      width=3
      group=main
    ]
@@ -72,7 +69,7 @@ these consist of cycles: :ref:`gmx grompp` -> :ref:`gmx mdrun`.
    grompp [
      label="Generate mdrun input file\ngmx grompp"
      tooltip="Process parameters, coordinates and topology and write binary topology"
-     URL="../programs/gmx-grompp.html"
+     URL="../onlinehelp/gmx-grompp.html"
      width=3
      group=main
    ]
@@ -94,7 +91,7 @@ these consist of cycles: :ref:`gmx grompp` -> :ref:`gmx mdrun`.
    mdrun [
      label="Run the simulation (EM or MD)\ngmx mdrun"
      tooltip="The moment you have all been waiting for! START YOUR MD RUN"
-     URL="../programs/gmx-mdrun.html"
+     URL="../onlinehelp/gmx-mdrun.html"
      width=3
      group=main
    ]
@@ -113,7 +110,7 @@ these consist of cycles: :ref:`gmx grompp` -> :ref:`gmx mdrun`.
    analysis [
      label="Analysis\ngmx ...\ngmx view"
      tooltip="Your favourite GROMACS analysis tool"
-     URL="../programs/bytopic.html"
+     URL="../onlinehelp/bytopic.html"
    ]
 
    mdrun -> analysis [
@@ -125,7 +122,7 @@ these consist of cycles: :ref:`gmx grompp` -> :ref:`gmx mdrun`.
    energy [
      label="Analysis\ngmx energy"
      tooltip="Energy plots, averages and fluctuations"
-     URL="../programs/gmx-energy.html"
+     URL="../onlinehelp/gmx-energy.html"
    ]
 
    mdrun -> energy [