share/html/online/flow.html

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   3 GROMACS Flow Chart
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   7 <H2>GROMACS Flow chart</H2>
   8 This is a flow chart of a typical GROMACS MD run of a protein
   9 in a box of water.
  10 A more detailed example is available in the
  11 <A HREF="getting_started.html">Getting Started</A>
  12 section. Several steps of energy minimization may be nescessary,
  13 these consist of cycles: grompp -> mdrun.
  14 <p>
  15
  16 <CENTER>
  17 <TABLE BORDER=0 CELLMARGIN=0 CELLPADDING=0 CELLSPACING=0>
  18
  19 <TR>
  20 <TD COLSPAN=2 ALIGN=RIGHT> <A HREF=pdb.html onMouseOver="window.status='Protein Databank file'; return true">eiwit.pdb</A></TD>
  21 <TD ALIGN=RIGHT>&nbsp;<IMG SRC=../gif/flow_leftrightdown.gif></TD>
  22 <TD></TD>
  23 <TD></TD>
  24 <TD></TD>
  25 </TR>
  26
  27 <TR>
  28 <TD COLSPAN=2 ALIGN=LEFT>Generate a GROMACS topology </TD>
  29 <TD></TD>
  30 <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>
  31 <TD><IMG SRC=../gif/flow_vrule.gif></TD>
  32 </TR>
  33
  34
  35 <TR>
  36 <TD></TD>
  37 <TD></TD>
  38 <TD></TD>
  39 <TD ALIGN=CENTER><IMG SRC=../gif/flow_vline.gif BORDER=0></TD>
  40 <TD WIDTH=20></TD>
  41 <TD ALIGN=CENTER><IMG SRC=../gif/flow_vline.gif></TD>
  42 </TR>
  43
  44 <TR>
  45 <TD></TD>
  46 <TD></TD>
  47 <TD></TD>
  48 <TD ALIGN=CENTER><A HREF=gro.html onMouseOver="window.status='GROMACS coordinate file containing molecules from PDB file'; return true">conf.gro</A></TD>
  49 <TD></TD>
  50 <TD ALIGN=CENTER> <A HREF=top.html onMouseOver="window.status='GROMACS ascii topology file'; return true">topol.top</A> </TD>
  51 </TR>
  52
  53 <TR>
  54 <TD></TD>
  55 <TD></TD>
  56 <TD></TD>
  57 <TD ALIGN=CENTER><IMG SRC=../gif/flow_down.gif BORDER=0></TD>
  58 <TD></TD>
  59 <TD ROWSPAN=5 COLSPAN=1 ALIGN=CENTER><IMG SRC=../gif/flow_vline.gif><BR><IMG SRC=../gif/flow_vline.gif><BR><IMG SRC=../gif/flow_vline.gif><BR><IMG SRC=../gif/flow_vline.gif><BR><IMG SRC=../gif/flow_down.gif></TD>
  60 </TR>
  61
  62 <TR>
  63 <TD COLSPAN=2 ALIGN=left>Enlarge the box</TD>
  64 <TD></TD>
  65 <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>
  66 <TD></TD>
  67 <TD><IMG SRC=../gif/flow_vrule.gif></TD>
  68 </TR>
  69
  70 <TR>
  71 <TD></TD>
  72 <TD></TD>
  73 <TD></TD>
  74 <TD ALIGN=CENTER><IMG SRC=../gif/flow_vline.gif></TD>
  75 <TD></TD>
  76 </TR>
  77
  78 <TR>
  79 <TD></TD>
  80 <TD></TD>
  81 <TD></TD>
  82 <TD ALIGN=CENTER> <A HREF=gro.html onMouseOver="window.status='GROMACS coordinate file with adjusted box etc.'; return true">conf.gro</A> </TD>
  83 <TD></TD>
  84 </TR>
  85
  86
  87 <TR>
  88 <TD></TD>
  89 <TD></TD>
  90 <TD></TD>
  91 <TD ALIGN=CENTER><IMG SRC=../gif/flow_down.gif></TD>
  92 <TD></TD>
  93 </TR>
  94
  95 <TR>
  96 <TD COLSPAN=2 ALIGN=LEFT>Solvate protein</TD>
  97 <TD></TD>
  98 <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>
  99 <TD><IMG SRC=../gif/flow_vrule.gif></TD>
 100 </TR>
 101
 102 <TR>
 103 <TD></TD>
 104 <TD></TD>
 105 <TD></TD>
 106 <TD ALIGN=CENTER><IMG SRC=../gif/flow_vline.gif></TD>
 107 <TD></TD>
 108 <TD ALIGN=CENTER><IMG SRC=../gif/flow_vline.gif></TD>
 109 </TR>
 110
 111 <TR>
 112 <TD></TD>
 113 <TD></TD>
 114 <TD></TD>
 115 <TD ALIGN=CENTER><A HREF=gro.html onMouseOver="window.status='GROMACS coordinate file with water molecules added'; return true">conf.gro</A></TD>
 116 <TD></TD>
 117 <TD ALIGN=CENTER> <A HREF=top.html onMouseOver="window.status='GROMACS ascii topology file with water molecules added'; return true">topol.top</A> </TD>
 118 </TR>
 119
 120 <TR>
 121 <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>
 122 <TD ALIGN=RIGHT>&nbsp;<IMG SRC=../gif/flow_leftrightdown.gif></TD>
 123 <TD ALIGN=CENTER><IMG SRC=../gif/flow_down.gif></TD>
 124 <TD></TD>
 125 <TD ALIGN=CENTER><IMG SRC=../gif/flow_down.gif></TD>
 126 <TD COLSPAN=3 ALIGN=CENTER VALIGN=BOTTOM><SMALL>(continuation)</SMALL></TD>
 127 </TR>
 128
 129
 130 <TR>
 131 <TD COLSPAN=2 ALIGN=LEFT>Generate mdrun input file</TD>
 132 <TD></TD>
 133 <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>
 134 <TD><IMG SRC=../gif/flow_vrule.gif></TD>
 135 <TD COLSPAN=2 ALIGN=CENTER><IMG SRC=../gif/flow_left.gif><IMG SRC=../gif/flow_hline.gif></TD>
 136 <TD ROWSPAN=2><IMG SRC=../gif/flow_downleft.gif><BR><IMG SRC=../gif/flow_vline.gif></TD>
 137 </TR>
 138
 139 <TR>
 140 <TD></TD>
 141 <TD></TD>
 142 <TD></TD>
 143 <TD></TD>
 144 <TD ALIGN=CENTER><IMG SRC=../gif/flow_vline.gif></TD>
 145 <TD ROWSPAN=3 ALIGN=CENTER><IMG SRC=../gif/flow_right+left.gif></TD>
 146 <TD COLSPAN=3 ALIGN=CENTER VALIGN=BOTTOM><SMALL>(after crash)</SMALL></TD>
 147 </TR>
 148
 149 <TR>
 150 <TD COLSPAN=2 ALIGN=LEFT></TD>
 151 <TD></TD>
 152 <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>
 153 <TD><IMG SRC=../gif/flow_vrule.gif></TD>
 154 <TD ALIGN=CENTER BGCOLOR=#777777>&nbsp;&nbsp;<A HREF=tpbconv.html onMouseOver="window.status='Rewrite binary topology with new coordinates and number of steps for restart after crash'; return true"><B>tpbconv</B></A>&nbsp;&nbsp;</TD>
 155 <TD>&nbsp;<IMG SRC=../gif/flow_left.gif>&nbsp;</TD>
 156 <TD ALIGN=CENTER><A HREF=trr.html onMouseOver="window.status='Full precision portable trajectory'; return true">traj.trr</A></TD>
 157 </TR>
 158
 159 <TR>
 160 <TD></TD>
 161 <TD></TD>
 162 <TD></TD>
 163 <TD></TD>
 164 <TD ALIGN=CENTER><IMG SRC=../gif/flow_down.gif></TD>
 165 <TD></TD>
 166 <TD></TD>
 167 <TD></TD>
 168 <TD ROWSPAN=2><IMG SRC=../gif/flow_vline.gif><BR><IMG SRC=../gif/flow_leftup.gif></TD>
 169 </TR>
 170
 171 <TR>
 172 <TD COLSPAN=2>Run the simulation (EM, MD or LD)</TD>
 173 <TD></TD>
 174 <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>
 175 <TD><IMG SRC=../gif/flow_vrule.gif></TD>
 176 <TD COLSPAN=2 ALIGN=CENTER><IMG SRC=../gif/flow_hline.gif><IMG SRC=../gif/flow_right.gif></TD>
 177 </TR>
 178
 179 <TR>
 180 <TD></TD>
 181 <TD></TD>
 182 <TD></TD>
 183 <TD ALIGN=CENTER><IMG SRC=../gif/flow_vline.gif></TD>
 184 <TD></TD>
 185 <TD ALIGN=CENTER><IMG SRC=../gif/flow_vline.gif></TD>
 186 </TR>
 187
 188 <TR>
 189 <TD></TD>
 190 <TD></TD>
 191 <TD></TD>
 192 <TD ALIGN=CENTER> <A HREF=xtc.html onMouseOver="window.status='Portable compressed trajectory'; return true">traj.xtc</A> </TD>
 193 <TD></TD>
 194 <TD ALIGN=CENTER> <A HREF=edr.html onMouseOver="window.status='Portable energy file'; return true">ener.edr</A> </TD>
 195 </TR>
 196
 197 <TR>
 198 <TD></TD>
 199 <TD></TD>
 200 <TD></TD>
 201 <TD ALIGN=CENTER><IMG SRC=../gif/flow_down.gif></TD>
 202 <TD></TD>
 203 <TD ALIGN=CENTER><IMG SRC=../gif/flow_down.gif></TD>
 204 </TR>
 205
 206 <TR>
 207 <TD COLSPAN=2 ALIGN=LEFT>Analysis</TD>
 208 <TD></TD>
 209 <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>
 210 <TD></TD>
 211 <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>
 212 <TD><IMG SRC=../gif/flow_vrule.gif></TD>
 213 </TR>
 214
 215
 216 </TABLE>
 217 </CENTER>
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