1 <TITLE>Flow Chart</TITLE>
2 <p>This is a flow chart of a typical GROMACS MD run of a protein
4 A more detailed example is available in the
5 <A HREF="getting_started.html">Getting Started</A>
6 section. Several steps of energy minimization may be necessary,
7 these consist of cycles: grompp -> mdrun.
11 <TABLE BORDER=0 CELLMARGIN=0 CELLPADDING=0 CELLSPACING=0>
14 <TD COLSPAN=2 ALIGN=RIGHT> <A HREF=pdb.html onMouseOver="window.status='Protein Databank file'; return true">eiwit.pdb</A></TD>
15 <TD ALIGN=RIGHT> <IMG SRC=../images/flow_leftrightdown.gif></TD>
22 <TD COLSPAN=2 ALIGN=LEFT>Generate a GROMACS topology </TD>
24 <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>
25 <TD><IMG SRC=../images/flow_vrule.gif></TD>
33 <TD ALIGN=CENTER><IMG SRC=../images/flow_vline.gif BORDER=0></TD>
35 <TD ALIGN=CENTER><IMG SRC=../images/flow_vline.gif></TD>
42 <TD ALIGN=CENTER><A HREF=gro.html onMouseOver="window.status='GROMACS coordinate file containing molecules from PDB file'; return true">conf.gro</A></TD>
44 <TD ALIGN=CENTER> <A HREF=top.html onMouseOver="window.status='GROMACS ascii topology file'; return true">topol.top</A> </TD>
51 <TD ALIGN=CENTER><IMG SRC=../images/flow_down.gif BORDER=0></TD>
53 <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>
57 <TD COLSPAN=2 ALIGN=left>Enlarge the box</TD>
59 <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>
61 <TD><IMG SRC=../images/flow_vrule.gif></TD>
68 <TD ALIGN=CENTER><IMG SRC=../images/flow_vline.gif></TD>
76 <TD ALIGN=CENTER> <A HREF=gro.html onMouseOver="window.status='GROMACS coordinate file with adjusted box etc.'; return true">conf.gro</A> </TD>
85 <TD ALIGN=CENTER><IMG SRC=../images/flow_down.gif></TD>
90 <TD COLSPAN=2 ALIGN=LEFT>Solvate protein</TD>
92 <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>
93 <TD><IMG SRC=../images/flow_vrule.gif></TD>
100 <TD ALIGN=CENTER><IMG SRC=../images/flow_vline.gif></TD>
102 <TD ALIGN=CENTER><IMG SRC=../images/flow_vline.gif></TD>
109 <TD ALIGN=CENTER><A HREF=gro.html onMouseOver="window.status='GROMACS coordinate file with water molecules added'; return true">conf.gro</A></TD>
111 <TD ALIGN=CENTER> <A HREF=top.html onMouseOver="window.status='GROMACS ascii topology file with water molecules added'; return true">topol.top</A> </TD>
115 <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>
116 <TD ALIGN=RIGHT> <IMG SRC=../images/flow_leftrightdown.gif></TD>
117 <TD ALIGN=CENTER><IMG SRC=../images/flow_down.gif></TD>
119 <TD ALIGN=CENTER><IMG SRC=../images/flow_down.gif></TD>
125 <TD COLSPAN=2 ALIGN=LEFT>Generate mdrun input file</TD>
127 <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>
128 <TD><IMG SRC=../images/flow_vrule.gif></TD>
138 <TD ALIGN=CENTER><IMG SRC=../images/flow_vline.gif></TD>
139 <TD ROWSPAN=3 ALIGN=RIGHT>
140 <IMG SRC=../images/flow_rightleftdown.gif></TD>
141 <TD ALIGN=CENTER VALIGN=BOTTOM>Continuation</TD>
145 <TD COLSPAN=2 ALIGN=LEFT></TD>
147 <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>
148 <TD ALIGN=CENTER > <A HREF=cpt.html onMouseOver="window.status='Checkpoint file'; return true">state.cpt</A> </TD>
156 <TD ALIGN=CENTER><IMG SRC=../images/flow_down.gif></TD>
157 <TD ROWSPAN=2 ALIGN=CENTER>
158 <IMG SRC=../images/flow_vline.gif><BR>
159 <IMG SRC=../images/flow_leftup.gif></TD>
163 <TD COLSPAN=2>Run the simulation (EM or MD)</TD>
165 <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>
173 <TD ALIGN=CENTER><IMG SRC=../images/flow_vline.gif></TD>
175 <TD ALIGN=CENTER><IMG SRC=../images/flow_vline.gif></TD>
182 <TD ALIGN=CENTER> <A HREF=xtc.html onMouseOver="window.status='Portable compressed trajectory'; return true">traj.xtc</A> /
183 <A HREF=trr.html onMouseOver="window.status='Full precision portable trajectory'; return true">traj.trr</A> </TD>
185 <TD ALIGN=CENTER> <A HREF=edr.html onMouseOver="window.status='Portable energy file'; return true">ener.edr</A> </TD>
192 <TD ALIGN=CENTER><IMG SRC=../images/flow_down.gif></TD>
194 <TD ALIGN=CENTER><IMG SRC=../images/flow_down.gif></TD>
198 <TD COLSPAN=2 ALIGN=LEFT>Analysis</TD>
200 <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>
202 <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>
203 <TD><IMG SRC=../images/flow_vrule.gif></TD>