share/html/online/getting_started.html

   1 <HTML>
   2 <HEAD>
   3 <TITLE>Getting started</TITLE>
   4 <LINK rel=stylesheet href="style.css" type="text/css">
   5 <BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
   6 <TABLE WIDTH="98%" NOBORDER >
   7 <TR><TD WIDTH=400>
   8 <TABLE WIDTH=400 NOBORDER>
   9 <TD WIDTH=116>
  10 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
  11 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>Getting started</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 <H3>Contents</H3>
  16
  17 <ul>
  18 <li><a href="#start">Introduction</a>
  19 <ul>
  20         <li><a href="#setup">Setting up your environment</a>
  21         <li><a href="#examples">Examples</a>
  22 </ul>
  23 <li><a href="gmxdemo.html">The GROMACS demo</a>
  24 <li><a href="water.html">Water</a>
  25 <li><a href="methanol.html">Methanol</a>
  26 <li><a href="mixed.html">Water/Methanol mixture</a>
  27 <li><a href="speptide.html">Ribonuclease S-Peptide</a>
  28 <li><a href="protunf.html">Protein unfolding</a>
  29 <li><a href="#files">GROMACS files</a>
  30 <ul>
  31         <li><a href="#top">Molecular topology file</a>
  32         <li><a href="#gro">Molecular structure file</a>
  33         <li><a href="#mdp">Molecular dynamics parameter file</a>
  34         <li><a href="#ndx">Index file</a>
  35         <li><a href="#tpr">Run input file</a>
  36         <li><a href="#trx">Trajectory file</a>
  37 </ul>
  38 <li><a href="#ref">References</a>
  39 </ul>
  40
  41 <P>
  42 More info can be found in the
  43 <A HREF="flow.html">flowchart</A>
  44 (for a quick overview) and the
  45 <A HREF="../gmxfaq.html">GMX FAQ</A>.
  46 </P>
  47
  48 <br><hr><br>
  49
  50 <a name="start"><H2>Introduction</A></H2>
  51 <p>
  52 In this chapter we assume the reader is familiar with Molecular
  53 Dynamics and familiar with Unix, including the use of a text editor
  54 such as <tt>jot</tt>, <tt>emacs</tt> or <tt>vi</tt>. We furthermore assume the
  55 GROMACS software is installed properly on your system. When you see a line
  56 like</p>
  57
  58 <table BORDER=0 CELLSPACING=0 CELLPADDING=8 COLS=3 WIDTH="100%" NOSAVE >
  59 <tr NOSAVE>
  60 <td WIDTH="2%" NOSAVE><font color="#000000"></font></td>
  61 <td WIDTH="80%" BGCOLOR="#000066" NOSAVE><font color="#FFFFFF">
  62
  63 <tt> ls -l
  64 </tt>
  65 <td></td>
  66 </tr>
  67 </table>
  68 <br>
  69 you are supposed to type the contents of that line on your computer.
  70
  71 <H3><A NAME="setup">Setting up your environment</A></H3>
  72 <p>
  73 In order to check whether you have access to the GROMACS software, please
  74 start by entering the command:
  75 </p>
  76 <table BORDER=0 CELLSPACING=0 CELLPADDING=8 COLS=3 WIDTH="100%" NOSAVE >
  77 <tr NOSAVE>
  78 <td WIDTH="2%" NOSAVE><font color="#000000"></font></td>
  79 <td WIDTH="80%" BGCOLOR="#000066" NOSAVE><font color="#FFFFFF">
  80
  81 <tt> luck
  82 </tt>
  83 <td></td>
  84 </tr>
  85 </table>
  86 <br>
  87 This command should return a cool quote like:
  88 <pre>
  89 "Whatever Happened to Pong ?" (F. Black)
  90 </pre>
  91
  92 If this, in contrast, returns the phrase
  93 <pre>
  94 luck: command not found.
  95 </pre>
  96
  97 then you have to verify where your version of GROMACS is installed.
  98
  99 In the default case, the binaries are located in
 100 '/usr/local/gromacs/&lt;arch&gt;/bin', where &lt;arch&gt; is the
 101 architecture of your computer. However, you can ask your local system
 102 administrator for more information.  If we assume that GROMACS is
 103 installed in directory <tt>XXX</tt> and your machine architecture is
 104 <tt>sgi</tt> you would find the executables (programs) in
 105 <tt>XXX/sgi/bin</tt>.  To be able to access the programs without
 106 problems, you will have to edit the login file for your shell. If you
 107 use the C shell, this file is called <TT>.cshrc</TT> or
 108 <TT>.tcshrc</TT>, and it is located in your home directory. Add a line
 109 like:
 110
 111 <br><br>
 112 <table BORDER=0 CELLSPACING=0 CELLPADDING=8 COLS=3 WIDTH="100%" NOSAVE >
 113 <tr NOSAVE>
 114 <td WIDTH="2%" NOSAVE><font color="#000000"></font></td>
 115 <td WIDTH="80%" BGCOLOR="#000066" NOSAVE><font color="#FFFFFF">
 116 <tt>
 117 setenv PATH "XXX/&lt;arch&gt;/bin:${PATH}".
 118 </tt>
 119 <td></td>
 120 </tr>
 121 </table>
 122 <br>
 123
 124 Issue this command at the prompt too, or log off and on again to
 125 automatically get the environment.
 126
 127 <P><H3><A NAME="examples">Examples</A></H3>
 128 Before starting the examples, you have to copy all the neccesary
 129 files, to your own directory. Chdir to the directory you want to put
 130 the examples directory. This directory (named <tt>tutor</tt>)
 131 will need
 132 about 20 MB of disk space, when it is completely filled.<br><br>
 133 <table BORDER=0 CELLSPACING=0 CELLPADDING=8 COLS=3 WIDTH="100%" NOSAVE >
 134 <tr NOSAVE>
 135 <td WIDTH="2%" NOSAVE><font color="#000000"></font></td>
 136 <td WIDTH="80%" BGCOLOR="#000066" NOSAVE><font color="#FFFFFF">
 137
 138 <tt> cd "your own directory"
 139 </tt>
 140 <td></td>
 141 </tr>
 142 </table>
 143 <br>
 144 then copy the examples: <br><br>
 145 <table BORDER=0 CELLSPACING=0 CELLPADDING=8 COLS=3 WIDTH="100%" NOSAVE >
 146 <tr NOSAVE>
 147 <td WIDTH="2%" NOSAVE><font color="#000000"></font></td>
 148 <td WIDTH="80%" BGCOLOR="#000066" NOSAVE><font color="#FFFFFF">
 149
 150 <tt> cp -r XXX/share/tutor .
 151 </tt>
 152 <td></td>
 153 </tr>
 154 </table>
 155 <br>
 156 (NOTE: include the "<TT>.</TT>", and replace <tt>XXX</tt> by the real directory)<br>
 157 If that directory doesn't exist you could look for the files
 158 in <tt>/usr/local/share/gromacs/tutor</tt>, or ask your local GROMACS expert.
 159 <br> You now have a subdirectory
 160 <tt>tutor</tt>. Move there<br><br>
 161 <table BORDER=0 CELLSPACING=0 CELLPADDING=8 COLS=3 WIDTH="100%" NOSAVE >
 162 <tr NOSAVE>
 163 <td WIDTH="2%" NOSAVE><font color="#000000"></font></td>
 164 <td WIDTH="80%" BGCOLOR="#000066" NOSAVE><font color="#FFFFFF">
 165
 166 <tt>  cd tutor
 167  </tt>
 168 <td></td>
 169 </tr>
 170 </table>
 171 <br>
 172 and view the contents of this directory
 173 <br><br>
 174 <table BORDER=0 CELLSPACING=0 CELLPADDING=8 COLS=3 WIDTH="100%" NOSAVE >
 175 <tr NOSAVE>
 176 <td WIDTH="2%" NOSAVE><font color="#000000"></font></td>
 177 <td WIDTH="80%" BGCOLOR="#000066" NOSAVE><font color="#FFFFFF">
 178
 179 <tt> ls -l
 180 </tt>
 181 <td></td>
 182 </tr>
 183 </table>
 184 <br>
 185 If all is well you will have seven subdirectories with examples
 186 with names like <tt>gmxdemo</tt>, <tt>methanol</tt>,
 187 <tt>mixed</tt>, <tt>nmr1</tt>, <tt>nmr2</tt>,
 188 <tt>speptide</tt> and <tt>water</tt>.
 189 <P>
 190 You are encouraged to look up the different programs and
 191 file formats in <a href="../online.html">
 192 the online manual</a> while you are browsing through the examples.</p>
 193
 194 <b>While going through the tutorial you will find questions
 195 (<font color="red">in a red font</font>). Try to answer them, to increase
 196 your understanding of molecular simulation.</b>
 197
 198
 199
 200 <a href="gmxdemo.html"><h3>Go to the first step</h3></a>
 201
 202 <br><hr><br>
 203 <H2><A NAME="files">GROMACS files</A></h2>
 204 Here is an overview of the most important GROMACS file types that you will
 205 encounter during the tutorial.
 206 <DL>
 207 <DT>
 208 <h3><A NAME="top">Molecular Topology file (<TT><a href="top.html">.top</a></TT>)</A></h3>
 209 <DD>
 210 The molecular topology file is generated by the program <TT>
 211 <a href="pdb2gmx.html">pdb2gmx</a></TT>. <a href="pdb2gmx.html">pdb2gmx</a> translates a <a href="pdb.html">pdb</a> structure file of any peptide
 212 or protein
 213 to a molecular topology file. This topology file contains a complete
 214 description of all the interactions in your peptide or protein.
 215 <P></P>
 216
 217 <DT>
 218 <h3><A NAME="gro">Molecular Structure file (<TT><a href="gro.html">.gro</a></TT>, <TT><a href="pdb.html">.pdb</a></TT>)</A></h3>
 219 <DD>
 220 When the <a href="pdb2gmx.html">pdb2gmx</a> program is executed to generate a molecular
 221 topology, it also translates the structure file (<TT><a href="pdb.html">.pdb</a></TT> file)
 222 to a gromos
 223 structure file (<TT><a href="gro.html">.gro</a></TT> file). The main difference between a
 224 <a href="pdb.html">pdb</a> file and a gromos file is their format and that
 225 a <TT><a href="gro.html">.gro</a></TT> file can also hold velocities. However, if you do not need the
 226 velocities, you can also use a <a href="pdb.html">pdb</a> file in all programs.
 227 To generate a box of solvent molecules
 228 around the peptide, the program
 229 <a href="genbox.html">genbox</a> is used. First the program
 230 <a href="editconf.html">editconf</a> should be used to
 231 define a box of appropriate size around the molecule.
 232 <a href="genbox.html">genbox</a>
 233 dissolves a solute molecule (the peptide) into any solvent (in this
 234 case water). The output of <TT><a href="genbox.html">genbox</a></TT> is a gromos structure file of
 235 the peptide dissolved in water. The <a href="genbox.html">genbox</a> program also changes the
 236 molecular topology file (generated by <a href="pdb2gmx.html">pdb2gmx</a>) to add solvent
 237 to the topology.
 238 <P></P>
 239
 240 <DT>
 241 <h3><A NAME="mdp">Molecular Dynamics parameter file (<TT><a href="mdp_opt.html">.mdp</a></TT>)</A></h3>
 242 <DD>
 243 The Molecular Dynamics Parameter (<TT><a href="mdp_opt.html">.mdp</a></TT>) file contains all
 244 information about the Molecular Dynamics simulation itself
 245 e.g. time-step, number of steps, temperature, pressure etc. The
 246 easiest way of handling such a file is by adapting a sample <TT><a href="mdp_opt.html">.mdp</a></TT>
 247 file. A <TT><a href="mdp.html">sample mdp file</a></TT>
 248 can be found online.
 249 <P></P>
 250
 251 <DT>
 252 <h3><A NAME="ndx">Index file (<TT><a href="ndx.html">.ndx</a></TT>)</A></h3>
 253 <DD>
 254 Sometimes you may need an index file to specify actions on groups of atoms
 255 (e.g. Temperature coupling, accelerations, freezing). Usually the default index
 256 groups will be sufficient, so for this demo we will
 257 not consider the use of index files.
 258 <P></P>
 259
 260 <DT>
 261 <h3><A NAME="tpr">Run input file (<TT><a href="tpr.html">.tpr</a></TT>)</A></h3>
 262 <DD>
 263 The next step is to combine the molecular structure (<TT><a href="gro.html">.gro</a></TT> file),
 264 topology (<TT><a href="top.html">.top</a></TT> file) MD-parameters (<TT><a href="mdp_opt.html">.mdp</a></TT> file) and
 265 (optionally) the
 266 index file (<TT><a href="ndx.html">ndx</a></TT>) to generate a run input file (<TT><a href="tpr.html">.tpr</a></tt> extension or
 267 <TT><a href="tpb.html">.tpb</a></tt> if you don't have XDR).
 268 This file contains all information needed to start a simulation with GROMACS.
 269 The <a href="grompp.html">
 270 grompp</a> program processes all input files and generates the run input
 271 <tt><a href="tpr.html">.tpr</a></tt> file.
 272 <P></P>
 273
 274 <DT>
 275 <h3><A NAME="trx">Trajectory file (<TT><a href="trr.html">.trr</a></TT></A>)</h3>
 276 <DD>
 277 Once the run input file is available, we can start the
 278 simulation. The program which starts the simulation is called
 279 <a href="mdrun.html">mdrun</a>. The only input file
 280 of <TT><a href="mdrun.html">mdrun</a></TT> you usually need to start a run
 281 is the run input file (<TT><a href="tpr.html">.tpr</a></TT> file).
 282 The output files of
 283 <TT><a href="mdrun.html">mdrun</a></TT> are the
 284 trajectory file (<TT><a href="trr.html">.trr</a></TT> file
 285 or <TT><a href="trj.html">.trj</a></TT> if you don't have XDR) and a logfile (
 286 <TT><a href="log.html">.log</A></TT> file).
 287 <P></P>
 288
 289 </DL>
 290
 291 <br><hr><br>
 292
 293 <P><H2><A NAME="ref">References</A></h2>
 294
 295 <blockquote>
 296 <dl>
 297
 298 <dt><A NAME="berendsen81">Berendsen, H.J.C., Postma, J.P.M., van
 299 Gunsteren, W.F., Hermans, J. (1981) <dd><it>Intermolecular
 300 Forces</it>, chapter Interaction models for water in relation to
 301 protein hydration, pp 331-342. Dordrecht: D. Reidel Publishing Company
 302 Dordrecht</dd><p>
 303
 304 <dt><A NAME="kabsch83">Kabsch, W., Sander, C. (1983). <dd>Dictionary
 305 of protein secondary structure: Pattern recognition of hydrogen-bonded
 306 and geometrical features. <it>Biopolymers</it> <b>22</b>,
 307 2577--2637.</dd><p>
 308
 309 <dt><A NAME="mierke91">Mierke, D.F., Kessler, H. (1991). <dd>Molecular
 310 dynamics with dimethyl sulfoxide as a solvent. Conformation of a
 311 cyclic hexapeptide. <it>J. Am. Chem. Soc.</it> <b>113</b>, 9446.</dd><p>
 312
 313 <dt><A NAME="stryer88">Stryer, L. (1988). <dd><it>Biochemistry</it>
 314 vol. 1, p. 211. New York: Freeman, 3 edition.</dd><p>
 315
 316 </dl>
 317 </blockquote>
 318
 319 <br>
 320 <hr>
 321 <div ALIGN=RIGHT>
 322 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
 323
 324 </div>
 325 </BODY>
 326 </HTML>