share/html/online/flow.html

   1 <TITLE>Flow Chart</TITLE>
   2 <p>This is a flow chart of a typical GROMACS MD run of a protein
   3 in a box of water.
   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 -&gt; mdrun.
   8 <p>
   9
  10 <CENTER>
  11 <TABLE BORDER=0 CELLMARGIN=0 CELLPADDING=0 CELLSPACING=0>
  12
  13 <TR>
  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>&nbsp;<IMG SRC=../images/flow_leftrightdown.gif></TD>
  16 <TD></TD>
  17 <TD></TD>
  18 <TD></TD>
  19 </TR>
  20
  21 <TR>
  22 <TD COLSPAN=2 ALIGN=LEFT>Generate a GROMACS topology </TD>
  23 <TD></TD>
  24 <TD BGCOLOR=#777777 COLSPAN=3 ALIGN=CENTER>&nbsp;<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>&nbsp;</TD>
  25 <TD><IMG SRC=../images/flow_vrule.gif></TD>
  26 </TR>
  27
  28
  29 <TR>
  30 <TD></TD>
  31 <TD></TD>
  32 <TD></TD>
  33 <TD ALIGN=CENTER><IMG SRC=../images/flow_vline.gif BORDER=0></TD>
  34 <TD WIDTH=20></TD>
  35 <TD ALIGN=CENTER><IMG SRC=../images/flow_vline.gif></TD>
  36 </TR>
  37
  38 <TR>
  39 <TD></TD>
  40 <TD></TD>
  41 <TD></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>
  43 <TD></TD>
  44 <TD ALIGN=CENTER> <A HREF=top.html onMouseOver="window.status='GROMACS ascii topology file'; return true">topol.top</A> </TD>
  45 </TR>
  46
  47 <TR>
  48 <TD></TD>
  49 <TD></TD>
  50 <TD></TD>
  51 <TD ALIGN=CENTER><IMG SRC=../images/flow_down.gif BORDER=0></TD>
  52 <TD></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>
  54 </TR>
  55
  56 <TR>
  57 <TD COLSPAN=2 ALIGN=left>Enlarge the box</TD>
  58 <TD></TD>
  59 <TD ALIGN=CENTER BGCOLOR=#777777>&nbsp;&nbsp;<A HREF=../programs/gmx-editconf.html onMouseOver="window.status='Adjust boxsize and placement of molecule'; return true"><B>gmx editconf</B></A>&nbsp;&nbsp;</TD>
  60 <TD></TD>
  61 <TD><IMG SRC=../images/flow_vrule.gif></TD>
  62 </TR>
  63
  64 <TR>
  65 <TD></TD>
  66 <TD></TD>
  67 <TD></TD>
  68 <TD ALIGN=CENTER><IMG SRC=../images/flow_vline.gif></TD>
  69 <TD></TD>
  70 </TR>
  71
  72 <TR>
  73 <TD></TD>
  74 <TD></TD>
  75 <TD></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>
  77 <TD></TD>
  78 </TR>
  79
  80
  81 <TR>
  82 <TD></TD>
  83 <TD></TD>
  84 <TD></TD>
  85 <TD ALIGN=CENTER><IMG SRC=../images/flow_down.gif></TD>
  86 <TD></TD>
  87 </TR>
  88
  89 <TR>
  90 <TD COLSPAN=2 ALIGN=LEFT>Solvate protein</TD>
  91 <TD></TD>
  92 <TD COLSPAN=3 ALIGN=CENTER BGCOLOR=#777777>&nbsp;<A HREF=../programs/gmx-solvate.html onMouseOver="window.status='Fill box with water (solvate molecule)'; return true"><B>gmx solvate</B></A>&nbsp;</TD>
  93 <TD><IMG SRC=../images/flow_vrule.gif></TD>
  94 </TR>
  95
  96 <TR>
  97 <TD></TD>
  98 <TD></TD>
  99 <TD></TD>
 100 <TD ALIGN=CENTER><IMG SRC=../images/flow_vline.gif></TD>
 101 <TD></TD>
 102 <TD ALIGN=CENTER><IMG SRC=../images/flow_vline.gif></TD>
 103 </TR>
 104
 105 <TR>
 106 <TD></TD>
 107 <TD></TD>
 108 <TD></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>
 110 <TD></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>
 112 </TR>
 113
 114 <TR>
 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>&nbsp;<IMG SRC=../images/flow_leftrightdown.gif></TD>
 117 <TD ALIGN=CENTER><IMG SRC=../images/flow_down.gif></TD>
 118 <TD></TD>
 119 <TD ALIGN=CENTER><IMG SRC=../images/flow_down.gif></TD>
 120 <TD></TD>
 121 </TR>
 122
 123
 124 <TR>
 125 <TD COLSPAN=2 ALIGN=LEFT>Generate mdrun input file</TD>
 126 <TD></TD>
 127 <TD COLSPAN=3 ALIGN=CENTER BGCOLOR=#777777>&nbsp; <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> &nbsp;</TD>
 128 <TD><IMG SRC=../images/flow_vrule.gif></TD>
 129 <TD></TD>
 130 <TD></TD>
 131 </TR>
 132
 133 <TR>
 134 <TD></TD>
 135 <TD></TD>
 136 <TD></TD>
 137 <TD></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>
 142 </TR>
 143
 144 <TR>
 145 <TD COLSPAN=2 ALIGN=LEFT></TD>
 146 <TD></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 >&nbsp;&nbsp;<A HREF=cpt.html onMouseOver="window.status='Checkpoint file'; return true">state.cpt</A>&nbsp;&nbsp;</TD>
 149 </TR>
 150
 151 <TR>
 152 <TD></TD>
 153 <TD></TD>
 154 <TD></TD>
 155 <TD></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>
 160 </TR>
 161
 162 <TR>
 163 <TD COLSPAN=2>Run the simulation (EM or MD)</TD>
 164 <TD></TD>
 165 <TD  COLSPAN=3 ALIGN=CENTER BGCOLOR=#777777>&nbsp;<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>&nbsp;</TD>
 166 <TD></TD>
 167 </TR>
 168
 169 <TR>
 170 <TD></TD>
 171 <TD></TD>
 172 <TD></TD>
 173 <TD ALIGN=CENTER><IMG SRC=../images/flow_vline.gif></TD>
 174 <TD></TD>
 175 <TD ALIGN=CENTER><IMG SRC=../images/flow_vline.gif></TD>
 176 </TR>
 177
 178 <TR>
 179 <TD></TD>
 180 <TD></TD>
 181 <TD></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>
 184 <TD></TD>
 185 <TD ALIGN=CENTER> <A HREF=edr.html onMouseOver="window.status='Portable energy file'; return true">ener.edr</A> </TD>
 186 </TR>
 187
 188 <TR>
 189 <TD></TD>
 190 <TD></TD>
 191 <TD></TD>
 192 <TD ALIGN=CENTER><IMG SRC=../images/flow_down.gif></TD>
 193 <TD></TD>
 194 <TD ALIGN=CENTER><IMG SRC=../images/flow_down.gif></TD>
 195 </TR>
 196
 197 <TR>
 198 <TD COLSPAN=2 ALIGN=LEFT>Analysis</TD>
 199 <TD></TD>
 200 <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=../programs/gmx-view.html onMouseOver="window.status='gmx view, the GROMACS trajectory viewer'; return true"><B>gmx view</B></A>&nbsp;&nbsp;</TD>
 201 <TD></TD>
 202 <TD ALIGN=CENTER BGCOLOR=#777777>&nbsp;&nbsp;<A HREF=../programs/gmx-energy.html onMouseOver="window.status='Energy plots, averages and  fluctuations'; return true"><B>gmx energy</B></A>&nbsp;&nbsp;</TD>
 203 <TD><IMG SRC=../images/flow_vrule.gif></TD>
 204 </TR>
 205
 206
 207 </TABLE>
 208 </CENTER>