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   3 <TITLE>Flow Chart</TITLE>
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  11 <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>
  12 </TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.0<br>
  13 Sun 18 Jan 2009</B></td></tr></TABLE>
  14 <HR>
  15 <p>This is a flow chart of a typical GROMACS MD run of a protein
  16 in a box of water.
  17 A more detailed example is available in the
  18 <A HREF="getting_started.html">Getting Started</A>
  19 section. Several steps of energy minimization may be necessary,
  20 these consist of cycles: grompp -> mdrun.
  21 <p>
  22
  23 <CENTER>
  24 <TABLE BORDER=0 CELLMARGIN=0 CELLPADDING=0 CELLSPACING=0>
  25
  26 <TR>
  27 <TD COLSPAN=2 ALIGN=RIGHT> <A HREF=pdb.html onMouseOver="window.status='Protein Databank file'; return true">eiwit.pdb</A></TD>
  28 <TD ALIGN=RIGHT>&nbsp;<IMG SRC=../images/flow_leftrightdown.gif></TD>
  29 <TD></TD>
  30 <TD></TD>
  31 <TD></TD>
  32 </TR>
  33
  34 <TR>
  35 <TD COLSPAN=2 ALIGN=LEFT>Generate a GROMACS topology </TD>
  36 <TD></TD>
  37 <TD BGCOLOR=#777777 COLSPAN=3 ALIGN=CENTER>&nbsp;<A HREF=pdb2gmx.html onMouseOver="window.status='Convert PDB file to GROMAX coordinate file and topology'; return true"><B>pdb2gmx</B></A>&nbsp;</TD>
  38 <TD><IMG SRC=../images/flow_vrule.gif></TD>
  39 </TR>
  40
  41
  42 <TR>
  43 <TD></TD>
  44 <TD></TD>
  45 <TD></TD>
  46 <TD ALIGN=CENTER><IMG SRC=../images/flow_vline.gif BORDER=0></TD>
  47 <TD WIDTH=20></TD>
  48 <TD ALIGN=CENTER><IMG SRC=../images/flow_vline.gif></TD>
  49 </TR>
  50
  51 <TR>
  52 <TD></TD>
  53 <TD></TD>
  54 <TD></TD>
  55 <TD ALIGN=CENTER><A HREF=gro.html onMouseOver="window.status='GROMACS coordinate file containing molecules from PDB file'; return true">conf.gro</A></TD>
  56 <TD></TD>
  57 <TD ALIGN=CENTER> <A HREF=top.html onMouseOver="window.status='GROMACS ascii topology file'; return true">topol.top</A> </TD>
  58 </TR>
  59
  60 <TR>
  61 <TD></TD>
  62 <TD></TD>
  63 <TD></TD>
  64 <TD ALIGN=CENTER><IMG SRC=../images/flow_down.gif BORDER=0></TD>
  65 <TD></TD>
  66 <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>
  67 </TR>
  68
  69 <TR>
  70 <TD COLSPAN=2 ALIGN=left>Enlarge the box</TD>
  71 <TD></TD>
  72 <TD ALIGN=CENTER BGCOLOR=#777777>&nbsp;&nbsp;<A HREF=editconf.html onMouseOver="window.status='Adjust boxsize and placement of molecule'; return true"><B>editconf</B></A>&nbsp;&nbsp;</TD>
  73 <TD></TD>
  74 <TD><IMG SRC=../images/flow_vrule.gif></TD>
  75 </TR>
  76
  77 <TR>
  78 <TD></TD>
  79 <TD></TD>
  80 <TD></TD>
  81 <TD ALIGN=CENTER><IMG SRC=../images/flow_vline.gif></TD>
  82 <TD></TD>
  83 </TR>
  84
  85 <TR>
  86 <TD></TD>
  87 <TD></TD>
  88 <TD></TD>
  89 <TD ALIGN=CENTER> <A HREF=gro.html onMouseOver="window.status='GROMACS coordinate file with adjusted box etc.'; return true">conf.gro</A> </TD>
  90 <TD></TD>
  91 </TR>
  92
  93
  94 <TR>
  95 <TD></TD>
  96 <TD></TD>
  97 <TD></TD>
  98 <TD ALIGN=CENTER><IMG SRC=../images/flow_down.gif></TD>
  99 <TD></TD>
 100 </TR>
 101
 102 <TR>
 103 <TD COLSPAN=2 ALIGN=LEFT>Solvate protein</TD>
 104 <TD></TD>
 105 <TD COLSPAN=3 ALIGN=CENTER BGCOLOR=#777777>&nbsp;<A HREF=genbox.html onMouseOver="window.status='Fill box with water (solvate molecule)'; return true"><B>genbox</B></A>&nbsp;</TD>
 106 <TD><IMG SRC=../images/flow_vrule.gif></TD>
 107 </TR>
 108
 109 <TR>
 110 <TD></TD>
 111 <TD></TD>
 112 <TD></TD>
 113 <TD ALIGN=CENTER><IMG SRC=../images/flow_vline.gif></TD>
 114 <TD></TD>
 115 <TD ALIGN=CENTER><IMG SRC=../images/flow_vline.gif></TD>
 116 </TR>
 117
 118 <TR>
 119 <TD></TD>
 120 <TD></TD>
 121 <TD></TD>
 122 <TD ALIGN=CENTER><A HREF=gro.html onMouseOver="window.status='GROMACS coordinate file with water molecules added'; return true">conf.gro</A></TD>
 123 <TD></TD>
 124 <TD ALIGN=CENTER> <A HREF=top.html onMouseOver="window.status='GROMACS ascii topology file with water molecules added'; return true">topol.top</A> </TD>
 125 </TR>
 126
 127 <TR>
 128 <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>
 129 <TD ALIGN=RIGHT>&nbsp;<IMG SRC=../images/flow_leftrightdown.gif></TD>
 130 <TD ALIGN=CENTER><IMG SRC=../images/flow_down.gif></TD>
 131 <TD></TD>
 132 <TD ALIGN=CENTER><IMG SRC=../images/flow_down.gif></TD>
 133 <TD></TD>
 134 </TR>
 135
 136
 137 <TR>
 138 <TD COLSPAN=2 ALIGN=LEFT>Generate mdrun input file</TD>
 139 <TD></TD>
 140 <TD COLSPAN=3 ALIGN=CENTER BGCOLOR=#777777>&nbsp; <A HREF=grompp.html onMouseOver="window.status='Process parameters, coordinates and topology and write binary topology'; return true"><B>grompp</B></A> &nbsp;</TD>
 141 <TD><IMG SRC=../images/flow_vrule.gif></TD>
 142 <TD></TD>
 143 <TD></TD>
 144 </TR>
 145
 146 <TR>
 147 <TD></TD>
 148 <TD></TD>
 149 <TD></TD>
 150 <TD></TD>
 151 <TD ALIGN=CENTER><IMG SRC=../images/flow_vline.gif></TD>
 152 <TD ROWSPAN=3 ALIGN=RIGHT>
 153 <IMG SRC=../images/flow_rightleftdown.gif></TD>
 154 <TD ALIGN=CENTER VALIGN=BOTTOM>Continuation</TD>
 155 </TR>
 156
 157 <TR>
 158 <TD COLSPAN=2 ALIGN=LEFT></TD>
 159 <TD></TD>
 160 <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>
 161 <TD ALIGN=CENTER >&nbsp;&nbsp;<A HREF=cpt.html onMouseOver="window.status='Checkpoint file'; return true">state.cpt</A>&nbsp;&nbsp;</TD>
 162 </TR>
 163
 164 <TR>
 165 <TD></TD>
 166 <TD></TD>
 167 <TD></TD>
 168 <TD></TD>
 169 <TD ALIGN=CENTER><IMG SRC=../images/flow_down.gif></TD>
 170 <TD ROWSPAN=2 ALIGN=CENTER>
 171 <IMG SRC=../images/flow_vline.gif><BR>
 172 <IMG SRC=../images/flow_leftup.gif></TD>
 173 </TR>
 174
 175 <TR>
 176 <TD COLSPAN=2>Run the simulation (EM or MD)</TD>
 177 <TD></TD>
 178 <TD  COLSPAN=3 ALIGN=CENTER BGCOLOR=#777777>&nbsp;<A HREF=mdrun.html onMouseOver="window.status='The moment you have all been waiting for! START YOUR MD RUN'; return true"><B>mdrun</B></A>&nbsp;</TD>
 179 <TD></TD>
 180 </TR>
 181
 182 <TR>
 183 <TD></TD>
 184 <TD></TD>
 185 <TD></TD>
 186 <TD ALIGN=CENTER><IMG SRC=../images/flow_vline.gif></TD>
 187 <TD></TD>
 188 <TD ALIGN=CENTER><IMG SRC=../images/flow_vline.gif></TD>
 189 </TR>
 190
 191 <TR>
 192 <TD></TD>
 193 <TD></TD>
 194 <TD></TD>
 195 <TD ALIGN=CENTER> <A HREF=xtc.html onMouseOver="window.status='Portable compressed trajectory'; return true">traj.xtc</A> /
 196 <A HREF=trr.html onMouseOver="window.status='Full precision portable trajectory'; return true">traj.trr</A> </TD>
 197 <TD></TD>
 198 <TD ALIGN=CENTER> <A HREF=edr.html onMouseOver="window.status='Portable energy file'; return true">ener.edr</A> </TD>
 199 </TR>
 200
 201 <TR>
 202 <TD></TD>
 203 <TD></TD>
 204 <TD></TD>
 205 <TD ALIGN=CENTER><IMG SRC=../images/flow_down.gif></TD>
 206 <TD></TD>
 207 <TD ALIGN=CENTER><IMG SRC=../images/flow_down.gif></TD>
 208 </TR>
 209
 210 <TR>
 211 <TD COLSPAN=2 ALIGN=LEFT>Analysis</TD>
 212 <TD></TD>
 213 <TD ALIGN=CENTER BGCOLOR=#777777>&nbsp;&nbsp;<A HREF=../online.html onMouseOver="window.status='Your favourite GROMACS analysis tool'; return true"><B>g_...</B></A>&nbsp;&nbsp;<BR>&nbsp;&nbsp;<A HREF=ngmx.html onMouseOver="window.status='ngmx, the GROMACS trajectory viewer'; return true"><B>ngmx</B></A>&nbsp;&nbsp;</TD>
 214 <TD></TD>
 215 <TD ALIGN=CENTER BGCOLOR=#777777>&nbsp;&nbsp;<A HREF=g_energy.html onMouseOver="window.status='Energy plots, averages and  fluctuations'; return true"><B>g_energy</B></A>&nbsp;&nbsp;</TD>
 216 <TD><IMG SRC=../images/flow_vrule.gif></TD>
 217 </TR>
 218
 219
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