The program help pages got moved from programs/ to onlinehelp/, but
these explicit links were forgotten.
Change-Id: Ia37f4b20d37f40f727835bca71d9b85f3260502c
Several steps of energy minimization may be necessary,
these consist of cycles: :ref:`gmx grompp` -> :ref:`gmx mdrun`.
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 ]
.. digraph:: flowchart
node [ shape=box, width=1.5 ]
pdb2gmx [
label="Generate a GROMACS topology\ngmx pdb2gmx"
tooltip="Convert PDB file to GROMACS coordinate file and topology"
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"
editconf [
label="Enlarge the box\ngmx editconf"
tooltip="Adjust box size and placement of molecule"
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"
solvate [
label="Solvate protein\ngmx solvate"
tooltip="Fill box with water (solvate molecule)"
solvate [
label="Solvate protein\ngmx solvate"
tooltip="Fill box with water (solvate molecule)"
- URL="../programs/gmx-solvate.html"
+ URL="../onlinehelp/gmx-solvate.html"
grompp [
label="Generate mdrun input file\ngmx grompp"
tooltip="Process parameters, coordinates and topology and write binary topology"
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"
mdrun [
label="Run the simulation (EM or MD)\ngmx mdrun"
tooltip="The moment you have all been waiting for! START YOUR MD RUN"
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"
analysis [
label="Analysis\ngmx ...\ngmx view"
tooltip="Your favourite GROMACS analysis tool"
analysis [
label="Analysis\ngmx ...\ngmx view"
tooltip="Your favourite GROMACS analysis tool"
- URL="../programs/bytopic.html"
+ URL="../onlinehelp/bytopic.html"
energy [
label="Analysis\ngmx energy"
tooltip="Energy plots, averages and fluctuations"
energy [
label="Analysis\ngmx energy"
tooltip="Energy plots, averages and fluctuations"
- URL="../programs/gmx-energy.html"
+ URL="../onlinehelp/gmx-energy.html"