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  11 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>Getting started - Water</h2>
  12 <font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
  13 </TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.0<br>
  14 Sun 18 Jan 2009</B></td></tr></TABLE>
  15 <HR>
  16
  17 <P><H2><A NAME="water">Water</A></H2>
  18 Now you are going to simulate 216 molecules of SPC water
  19 (<A HREF="getting_started.html#berendsen81">Berendsen <it>et al.</it>, 1981</A>)
  20 in a cubic box. In this example the GROMACS
  21 software team already generated most of the neccesary input
  22 files. The files needed in this example are:
  23 <ul>
  24 <LI> Initial structure of a box of 216 water molecules (<TT><a href="gro.html">.gro</a></TT>)</li>
  25
  26 <LI> Topology file of water (<tt><a href="top.html">.top</a></tt>)</li>
  27 <LI> Molecular Dynamics parameter file (<TT><a href="mdp_opt.html">.mdp</a></TT>)</li>
  28 </ul>
  29 <P>
  30 Change your directory to <tt>tutor/water </tt>:
  31 <br><br>
  32 <table BORDER=0 CELLSPACING=0 CELLPADDING=8 COLS=3 WIDTH="100%" NOSAVE >
  33 <tr NOSAVE>
  34 <td WIDTH="2%" NOSAVE><font color="#000000"></font></td>
  35 <td WIDTH="80%" BGCOLOR="#000066" NOSAVE><font color="#FFFFFF">
  36
  37 <tt> cd tutor/water</tt>
  38 <td></td>
  39 </tr>
  40 </table>
  41 <br>
  42 Let's first have a look at the coordinate file:
  43 <br><br>
  44 <table BORDER=0 CELLSPACING=0 CELLPADDING=8 COLS=3 WIDTH="100%" NOSAVE >
  45 <tr NOSAVE>
  46 <td WIDTH="2%" NOSAVE><font color="#000000"></font></td>
  47 <td WIDTH="80%" BGCOLOR="#000066" NOSAVE><font color="#FFFFFF">
  48
  49 <tt>  more conf.gro
  50 </tt>
  51 <td></td>
  52 </tr>
  53 </table>
  54 <br>
  55 Or to view the water box graphically:
  56 <br><br>
  57 <table BORDER=0 CELLSPACING=0 CELLPADDING=8 COLS=3 WIDTH="100%" NOSAVE >
  58 <tr NOSAVE>
  59 <td WIDTH="2%" NOSAVE><font color="#000000"></font></td>
  60 <td WIDTH="80%" BGCOLOR="#000066" NOSAVE><font color="#FFFFFF">
  61
  62 <tt>  rasmol spc216.pdb
  63 </tt>
  64 <td></td>
  65 </tr>
  66 </table>
  67 <br>
  68
  69 Have a look at the topology file:
  70 <br><br>
  71 <table BORDER=0 CELLSPACING=0 CELLPADDING=8 COLS=3 WIDTH="100%" NOSAVE >
  72 <tr NOSAVE>
  73 <td WIDTH="2%" NOSAVE><font color="#000000"></font></td>
  74 <td WIDTH="80%" BGCOLOR="#000066" NOSAVE><font color="#FFFFFF">
  75
  76 <tt>  more topol.top
  77 </tt>
  78 <td></td>
  79 </tr>
  80 </table>
  81 <br>
  82
  83 Have a look at the <a href="mdp_opt.html">MD-parameters file</a>:
  84 <br><br>
  85 <table BORDER=0 CELLSPACING=0 CELLPADDING=8 COLS=3 WIDTH="100%" NOSAVE >
  86 <tr NOSAVE>
  87 <td WIDTH="2%" NOSAVE><font color="#000000"></font></td>
  88 <td WIDTH="80%" BGCOLOR="#000066" NOSAVE><font color="#FFFFFF">
  89
  90 <tt>  more grompp.mdp
  91 </tt>
  92 <td></td>
  93 </tr>
  94 </table>
  95 <br>
  96
  97 Since all the neccesary files are available, we are going to
  98 preprocess the input files to create a run input
  99 (<TT><a href="tpr.html">.tpr</a></TT>) file.
 100 This run input file is the only input file for the
 101 MD-program <TT><a href="mdrun.html">mdrun</a></TT>.
 102 <br><br>
 103 <table BORDER=0 CELLSPACING=0 CELLPADDING=8 COLS=3 WIDTH="100%" NOSAVE >
 104 <tr NOSAVE>
 105 <td WIDTH="2%" NOSAVE><font color="#000000"></font></td>
 106 <td WIDTH="80%" BGCOLOR="#000066" NOSAVE><font color="#FFFFFF">
 107
 108 <tt>  grompp -v
 109 </tt>
 110 <td></td>
 111 </tr>
 112 </table>
 113 <br>
 114
 115 The run input file is only viewable with the program
 116 <TT><a href="gmxdump.html">gmxdump</a></TT>.
 117 In this way it is possible to check if the  preprocessor
 118 <TT><a href="grompp.html">grompp</a></TT> worked well.
 119 The output may seem rather cryptic, so don't panic when you don't
 120 understand every single item in it.
 121 <br><br>
 122 <table BORDER=0 CELLSPACING=0 CELLPADDING=8 COLS=3 WIDTH="100%" NOSAVE >
 123 <tr NOSAVE>
 124 <td WIDTH="2%" NOSAVE><font color="#000000"></font></td>
 125 <td WIDTH="80%" BGCOLOR="#000066" NOSAVE><font color="#FFFFFF">
 126
 127 <tt>  gmxdump -s topol.tpr | more
 128 </tt>
 129 <td></td>
 130 </tr>
 131 </table>
 132 <br>
 133
 134 Now it's time to start the simulation of 20 picoseconds.
 135 <br><br>
 136 <table BORDER=0 CELLSPACING=0 CELLPADDING=8 COLS=3 WIDTH="100%" NOSAVE >
 137 <tr NOSAVE>
 138 <td WIDTH="2%" NOSAVE><font color="#000000"></font></td>
 139 <td WIDTH="80%" BGCOLOR="#000066" NOSAVE><font color="#FFFFFF">
 140
 141 <tt> mdrun -v
 142 </tt>
 143 <td></td>
 144 </tr>
 145 </table>
 146 <br>
 147
 148 After the MD simulation is finished, it is possible to view the
 149 trajectory with the <a href="ngmx.html">ngmx</a> program:
 150 <br><br>
 151 <table BORDER=0 CELLSPACING=0 CELLPADDING=8 COLS=3 WIDTH="100%" NOSAVE >
 152 <tr NOSAVE>
 153 <td WIDTH="2%" NOSAVE><font color="#000000"></font></td>
 154 <td WIDTH="80%" BGCOLOR="#000066" NOSAVE><font color="#FFFFFF">
 155
 156 <tt> ngmx
 157 </tt>
 158 <td></td>
 159 </tr>
 160 </table>
 161 <br>
 162
 163 <P>
 164 When the program starts, you must select a group of atoms to view. In
 165 our case that will be "SOL" (for solvent) or "System", which is the
 166 same for a box of water as we have. Select one and click OK. Then
 167 select Display->Animate from the menu. Use the buttons to see your
 168 water moving (note: "Play" steps one frame forward; "Fast Forward"
 169 plays; "Rewind" skips back to the beginning of the trajectory).
 170 </P>
 171
 172 <hr>
 173 <h2>Analysis of the simulation</h2>
 174 <ol>
 175 <li><p>
 176 Calculate a radial distribution function of the Oxygen atoms. The
 177 index file <TT><a href="ndx.html">index.ndx</a></TT>
 178 contains one group with all the oxygen atoms.
 179 <br><br>
 180 <table BORDER=0 CELLSPACING=0 CELLPADDING=8 COLS=3 WIDTH="100%" NOSAVE >
 181 <tr NOSAVE>
 182 <td WIDTH="2%" NOSAVE><font color="#000000"></font></td>
 183 <td WIDTH="80%" BGCOLOR="#000066" NOSAVE><font color="#FFFFFF">
 184
 185 <tt> g_rdf -n index
 186 </tt>
 187 <td></td>
 188 </tr>
 189 </table>
 190 <br>
 191 The program will ask you for how many groups you want the calculate
 192 the RDF, answer 1. Now,
 193 view the output graph of <TT><a href="g_rdf.html">g_rdf</a></TT>.
 194 The file is already prepared to produce a nice graph in the
 195 <tt>xmgrace</tt> program.
 196 <br><br>
 197 <table BORDER=0 CELLSPACING=0 CELLPADDING=8 COLS=3 WIDTH="100%" NOSAVE >
 198 <tr NOSAVE>
 199 <td WIDTH="2%" NOSAVE><font color="#000000"></font></td>
 200 <td WIDTH="80%" BGCOLOR="#000066" NOSAVE><font color="#FFFFFF">
 201
 202 <tt> xmgrace rdf.xvg
 203 </tt>
 204 <td></td>
 205 </tr>
 206 </table>
 207 <br>
 208 Which shows you the radial distribution function for Oxygen-Oxygen in
 209 SPC water. The first peak is at roughly 0.28 nm, and has a height of 2.8.
 210 This means that the relative density of oxygen atoms in water,
 211 is almost 3 times higher at a distance of 0.28 nm from another oxygen atom.
 212 Obviously this is due to strong hydrogen bonding in liquid water.
 213 </P></li>
 214
 215 <li><p>
 216 We can also do a direct analysis of the number of hydrogen bonds in
 217 liquid water, based on O-O distance and O-H ... O angle.
 218 <br><br>
 219 <table BORDER=0 CELLSPACING=0 CELLPADDING=8 COLS=3 WIDTH="100%" NOSAVE >
 220 <tr NOSAVE>
 221 <td WIDTH="2%" NOSAVE><font color="#000000"></font></td>
 222 <td WIDTH="80%" BGCOLOR="#000066" NOSAVE><font color="#FFFFFF">
 223
 224 <tt> g_hbond
 225 </tt>
 226 <td></td>
 227 </tr>
 228 </table>
 229 <br>
 230 Select twice 0, when asked. Check the output with
 231 <br><br>
 232 <table BORDER=0 CELLSPACING=0 CELLPADDING=8 COLS=3 WIDTH="100%" NOSAVE >
 233 <tr NOSAVE>
 234 <td WIDTH="2%" NOSAVE><font color="#000000"></font></td>
 235 <td WIDTH="80%" BGCOLOR="#000066" NOSAVE><font color="#FFFFFF">
 236
 237 <tt> xmgrace hbnum.xvg
 238 </tt>
 239 <td></td>
 240 </tr>
 241 </table>
 242 <br>
 243 <font color="red">What is the number of hydrogen bonds per water
 244 molecule? What is the maximum possible number?</font>
 245 </p></li>
 246
 247 <li><p>
 248 As a further test of the simulation we will compute the self diffusion constant
 249 of water. This can be computed from the <b>Mean square displacement</b> (MSD)
 250 function. The MSD determines how much on average a molecule has moved
 251 with time. After a certain time period there is no correlation between the
 252 starting position and the current position and the square displacement will
 253 be linear with time. The slope of the MSD function is the linearly proportional
 254 to the self diffusion constant.
 255 <br><br>
 256 <table BORDER=0 CELLSPACING=0 CELLPADDING=8 COLS=3 WIDTH="100%" NOSAVE >
 257 <tr NOSAVE>
 258 <td WIDTH="2%" NOSAVE><font color="#000000"></font></td>
 259 <td WIDTH="80%" BGCOLOR="#000066" NOSAVE><font color="#FFFFFF">
 260
 261 <tt> g_msd -n index
 262 </tt>
 263 <td></td>
 264 </tr>
 265 </table>
 266 <br>
 267 View the output
 268 <br><br>
 269 <table BORDER=0 CELLSPACING=0 CELLPADDING=8 COLS=3 WIDTH="100%" NOSAVE >
 270 <tr NOSAVE>
 271 <td WIDTH="2%" NOSAVE><font color="#000000"></font></td>
 272 <td WIDTH="80%" BGCOLOR="#000066" NOSAVE><font color="#FFFFFF">
 273
 274 <tt> xmgrace msd.xvg
 275 </tt>
 276 <td></td>
 277 </tr>
 278 </table>
 279 <br>
 280 Check that the graph is roughly linear. The <tt>g_msd</tt> program also
 281 computes the diffusion constant D for you. The experimental value
 282 is roughly 2.3 x 10<sup>-5</sup> cm<sup>2</sup>/s. The simulation
 283 result is clearly too high, due to the simplicity of the model.
 284 </p></li>
 285 </ol>
 286
 287 <hr>
 288 <a href="methanol.html"><h3>Go to the next step</h3></a>
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