-<TITLE>Flow Chart</TITLE>
-<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="../user-guide/index.html#getting-started-with-gromacs">Getting Started</A>
-section. Several steps of energy minimization may be necessary,
-these consist of cycles: grompp -> mdrun.
-<p>
-
-<CENTER>
-<TABLE BORDER=0 CELLMARGIN=0 CELLPADDING=0 CELLSPACING=0>
-
-<TR>
-<TD COLSPAN=2 ALIGN=RIGHT> <A HREF=pdb.html onMouseOver="window.status='Protein Databank file'; return true">eiwit.pdb</A></TD>
-<TD ALIGN=RIGHT> <IMG SRC=../images/flow_leftrightdown.gif></TD>
-<TD></TD>
-<TD></TD>
-<TD></TD>
-</TR>
-
-<TR>
-<TD COLSPAN=2 ALIGN=LEFT>Generate a GROMACS topology </TD>
-<TD></TD>
-<TD BGCOLOR=#777777 COLSPAN=3 ALIGN=CENTER> <A HREF=../programs/gmx-pdb2gmx.html onMouseOver="window.status='Convert PDB file to GROMAX coordinate file and topology'; return true"><B>gmx pdb2gmx</B></A> </TD>
-<TD><IMG SRC=../images/flow_vrule.gif></TD>
-</TR>
-
-
-<TR>
-<TD></TD>
-<TD></TD>
-<TD></TD>
-<TD ALIGN=CENTER><IMG SRC=../images/flow_vline.gif BORDER=0></TD>
-<TD WIDTH=20></TD>
-<TD ALIGN=CENTER><IMG SRC=../images/flow_vline.gif></TD>
-</TR>
-
-<TR>
-<TD></TD>
-<TD></TD>
-<TD></TD>
-<TD ALIGN=CENTER><A HREF=gro.html onMouseOver="window.status='GROMACS coordinate file containing molecules from PDB file'; return true">conf.gro</A></TD>
-<TD></TD>
-<TD ALIGN=CENTER> <A HREF=top.html onMouseOver="window.status='GROMACS ascii topology file'; return true">topol.top</A> </TD>
-</TR>
-
-<TR>
-<TD></TD>
-<TD></TD>
-<TD></TD>
-<TD ALIGN=CENTER><IMG SRC=../images/flow_down.gif BORDER=0></TD>
-<TD></TD>
-<TD ROWSPAN=5 COLSPAN=1 ALIGN=CENTER><IMG SRC=../images/flow_vline.gif><BR><IMG SRC=../images/flow_vline.gif><BR><IMG SRC=../images/flow_vline.gif><BR><IMG SRC=../images/flow_vline.gif><BR><IMG SRC=../images/flow_down.gif></TD>
-</TR>
-
-<TR>
-<TD COLSPAN=2 ALIGN=left>Enlarge the box</TD>
-<TD></TD>
-<TD ALIGN=CENTER BGCOLOR=#777777> <A HREF=../programs/gmx-editconf.html onMouseOver="window.status='Adjust boxsize and placement of molecule'; return true"><B>gmx editconf</B></A> </TD>
-<TD></TD>
-<TD><IMG SRC=../images/flow_vrule.gif></TD>
-</TR>
-
-<TR>
-<TD></TD>
-<TD></TD>
-<TD></TD>
-<TD ALIGN=CENTER><IMG SRC=../images/flow_vline.gif></TD>
-<TD></TD>
-</TR>
-
-<TR>
-<TD></TD>
-<TD></TD>
-<TD></TD>
-<TD ALIGN=CENTER> <A HREF=gro.html onMouseOver="window.status='GROMACS coordinate file with adjusted box etc.'; return true">conf.gro</A> </TD>
-<TD></TD>
-</TR>
-
-
-<TR>
-<TD></TD>
-<TD></TD>
-<TD></TD>
-<TD ALIGN=CENTER><IMG SRC=../images/flow_down.gif></TD>
-<TD></TD>
-</TR>
-
-<TR>
-<TD COLSPAN=2 ALIGN=LEFT>Solvate protein</TD>
-<TD></TD>
-<TD COLSPAN=3 ALIGN=CENTER BGCOLOR=#777777> <A HREF=../programs/gmx-solvate.html onMouseOver="window.status='Fill box with water (solvate molecule)'; return true"><B>gmx solvate</B></A> </TD>
-<TD><IMG SRC=../images/flow_vrule.gif></TD>
-</TR>
-
-<TR>
-<TD></TD>
-<TD></TD>
-<TD></TD>
-<TD ALIGN=CENTER><IMG SRC=../images/flow_vline.gif></TD>
-<TD></TD>
-<TD ALIGN=CENTER><IMG SRC=../images/flow_vline.gif></TD>
-</TR>
-
-<TR>
-<TD></TD>
-<TD></TD>
-<TD></TD>
-<TD ALIGN=CENTER><A HREF=gro.html onMouseOver="window.status='GROMACS coordinate file with water molecules added'; return true">conf.gro</A></TD>
-<TD></TD>
-<TD ALIGN=CENTER> <A HREF=top.html onMouseOver="window.status='GROMACS ascii topology file with water molecules added'; return true">topol.top</A> </TD>
-</TR>
-
-<TR>
-<TD COLSPAN=2 ALIGN=RIGHT><A HREF=mdp.html onMouseOver="window.status='Parameter file for grompp (controls all MD parameters)'; return true">grompp.mdp</A></TD>
-<TD ALIGN=RIGHT> <IMG SRC=../images/flow_leftrightdown.gif></TD>
-<TD ALIGN=CENTER><IMG SRC=../images/flow_down.gif></TD>
-<TD></TD>
-<TD ALIGN=CENTER><IMG SRC=../images/flow_down.gif></TD>
-<TD></TD>
-</TR>
-
-
-<TR>
-<TD COLSPAN=2 ALIGN=LEFT>Generate mdrun input file</TD>
-<TD></TD>
-<TD COLSPAN=3 ALIGN=CENTER BGCOLOR=#777777> <A HREF=../programs/gmx-grompp.html onMouseOver="window.status='Process parameters, coordinates and topology and write binary topology'; return true"><B>gmx grompp</B></A> </TD>
-<TD><IMG SRC=../images/flow_vrule.gif></TD>
-<TD></TD>
-<TD></TD>
-</TR>
-
-<TR>
-<TD></TD>
-<TD></TD>
-<TD></TD>
-<TD></TD>
-<TD ALIGN=CENTER><IMG SRC=../images/flow_vline.gif></TD>
-<TD ROWSPAN=3 ALIGN=RIGHT>
-<IMG SRC=../images/flow_rightleftdown.gif></TD>
-<TD ALIGN=CENTER VALIGN=BOTTOM>Continuation</TD>
-</TR>
-
-<TR>
-<TD COLSPAN=2 ALIGN=LEFT></TD>
-<TD></TD>
-<TD COLSPAN=3 ALIGN=CENTER> <A HREF=tpr.html onMouseOver="window.status='Portable GROMACS binary run input file (contains all information to start MD run)'; return true">topol.tpr</A></TD>
-<TD ALIGN=CENTER > <A HREF=cpt.html onMouseOver="window.status='Checkpoint file'; return true">state.cpt</A> </TD>
-</TR>
-
-<TR>
-<TD></TD>
-<TD></TD>
-<TD></TD>
-<TD></TD>
-<TD ALIGN=CENTER><IMG SRC=../images/flow_down.gif></TD>
-<TD ROWSPAN=2 ALIGN=CENTER>
-<IMG SRC=../images/flow_vline.gif><BR>
-<IMG SRC=../images/flow_leftup.gif></TD>
-</TR>
-
-<TR>
-<TD COLSPAN=2>Run the simulation (EM or MD)</TD>
-<TD></TD>
-<TD COLSPAN=3 ALIGN=CENTER BGCOLOR=#777777> <A HREF=../programs/gmx-mdrun.html onMouseOver="window.status='The moment you have all been waiting for! START YOUR MD RUN'; return true"><B>gmx mdrun</B></A> </TD>
-<TD></TD>
-</TR>
-
-<TR>
-<TD></TD>
-<TD></TD>
-<TD></TD>
-<TD ALIGN=CENTER><IMG SRC=../images/flow_vline.gif></TD>
-<TD></TD>
-<TD ALIGN=CENTER><IMG SRC=../images/flow_vline.gif></TD>
-</TR>
-
-<TR>
-<TD></TD>
-<TD></TD>
-<TD></TD>
-<TD ALIGN=CENTER> <A HREF=xtc.html onMouseOver="window.status='Portable compressed trajectory'; return true">traj.xtc</A> /
-<A HREF=trr.html onMouseOver="window.status='Full precision portable trajectory'; return true">traj.trr</A> </TD>
-<TD></TD>
-<TD ALIGN=CENTER> <A HREF=edr.html onMouseOver="window.status='Portable energy file'; return true">ener.edr</A> </TD>
-</TR>
-
-<TR>
-<TD></TD>
-<TD></TD>
-<TD></TD>
-<TD ALIGN=CENTER><IMG SRC=../images/flow_down.gif></TD>
-<TD></TD>
-<TD ALIGN=CENTER><IMG SRC=../images/flow_down.gif></TD>
-</TR>
-
-<TR>
-<TD COLSPAN=2 ALIGN=LEFT>Analysis</TD>
-<TD></TD>
-<TD ALIGN=CENTER BGCOLOR=#777777> <A HREF=../online.html onMouseOver="window.status='Your favourite GROMACS analysis tool'; return true"><B>g_...</B></A> <BR> <A HREF=../programs/gmx-view.html onMouseOver="window.status='gmx view, the GROMACS trajectory viewer'; return true"><B>gmx view</B></A> </TD>
-<TD></TD>
-<TD ALIGN=CENTER BGCOLOR=#777777> <A HREF=../programs/gmx-energy.html onMouseOver="window.status='Energy plots, averages and fluctuations'; return true"><B>gmx energy</B></A> </TD>
-<TD><IMG SRC=../images/flow_vrule.gif></TD>
-</TR>
-
-
-</TABLE>
-</CENTER>