share/html/online/getting_started.html

   1 <TITLE>Getting started</TITLE>
   2 <H3>Contents</H3>
   3
   4 <ul>
   5 <li><a href="#start">Introduction</a>
   6 <ul>
   7         <li><a href="#setup">Setting up your environment</a>
   8 </ul>
   9 <li><a href="#files">GROMACS files</a>
  10 <ul>
  11         <li><a href="#top">Molecular topology file</a>
  12         <li><a href="#gro">Molecular structure file</a>
  13         <li><a href="#mdp">Molecular dynamics parameter file</a>
  14         <li><a href="#ndx">Index file</a>
  15         <li><a href="#tpr">Run input file</a>
  16         <li><a href="#trx">Trajectory file</a>
  17 </ul>
  18 <li><a href="#ref">References</a>
  19 </ul>
  20
  21 <P>
  22 More info can be found in the
  23 <A HREF="flow.html">flowchart</A>
  24 (for a quick overview) and the
  25 <A HREF="http://www.gromacs.org/Documentation/FAQs">GROMACS FAQs</A>.
  26 </P>
  27
  28 <br><hr><br>
  29
  30 <a name="start"><H2>Introduction</A></H2>
  31 <p>
  32 In this chapter we assume the reader is familiar with Molecular
  33 Dynamics and familiar with Unix, including the use of a text editor
  34 such as <tt>jot</tt>, <tt>emacs</tt> or <tt>vi</tt>. We furthermore assume the
  35 GROMACS software is installed properly on your system. When you see a line
  36 like</p>
  37
  38 <table BORDER=0 CELLSPACING=0 CELLPADDING=8 COLS=3 WIDTH="100%" NOSAVE >
  39 <tr NOSAVE>
  40 <td WIDTH="2%" NOSAVE><font color="#000000"></font></td>
  41 <td WIDTH="80%" BGCOLOR="#000066" NOSAVE><font color="#FFFFFF">
  42
  43 <tt> ls -l
  44 </tt>
  45 <td></td>
  46 </tr>
  47 </table>
  48 <br>
  49 you are supposed to type the contents of that line on your computer.
  50
  51 <H3><A NAME="setup">Setting up your environment</A></H3>
  52 <p>
  53 In order to check whether you have access to the GROMACS software, please
  54 start by entering the command:
  55 </p>
  56 <table BORDER=0 CELLSPACING=0 CELLPADDING=8 COLS=3 WIDTH="100%" NOSAVE >
  57 <tr NOSAVE>
  58 <td WIDTH="2%" NOSAVE><font color="#000000"></font></td>
  59 <td WIDTH="80%" BGCOLOR="#000066" NOSAVE><font color="#FFFFFF">
  60
  61 <tt> mdrun -version
  62 </tt>
  63 <td></td>
  64 </tr>
  65 </table>
  66 <br>
  67 This command should print out information about the version of Gromacs
  68 installed.
  69
  70 If this, in contrast, returns the phrase
  71 <pre>
  72 mdrun: command not found.
  73 </pre>
  74
  75 then you have to verify where your version of GROMACS is installed.
  76
  77 In the default case, the binaries are located in
  78 '/usr/local/gromacs/bin', however, you can ask your local system
  79 administrator for more information.  If we assume that GROMACS is
  80 installed in directory <tt>XXX</tt> you would find the executables (programs) in
  81 <tt>XXX/bin</tt>.  To be able to access the programs without
  82 problems, you will have to edit the login file for your shell. If you
  83 use the C shell, this file is called <TT>.cshrc</TT> or
  84 <TT>.tcshrc</TT>, and it is located in your home directory. Add a line
  85 like:
  86
  87 <br><br>
  88 <table BORDER=0 CELLSPACING=0 CELLPADDING=8 COLS=3 WIDTH="100%" NOSAVE >
  89 <tr NOSAVE>
  90 <td WIDTH="2%" NOSAVE><font color="#000000"></font></td>
  91 <td WIDTH="80%" BGCOLOR="#000066" NOSAVE><font color="#FFFFFF">
  92 <tt>
  93 source XXX/bin/GMXRC
  94 </tt>
  95 <td></td>
  96 </tr>
  97 </table>
  98 <br>
  99
 100 Issue this command at the prompt too, or log off and on again to
 101 automatically get the environment.
 102 You should have an environment variable set now that is called
 103 GMXDATA that we will use further on. Let us check whether this was
 104 successful using:<br><br>
 105
 106 <table BORDER=0 CELLSPACING=0 CELLPADDING=8 COLS=3 WIDTH="100%" NOSAVE >
 107 <tr NOSAVE>
 108 <td WIDTH="2%" NOSAVE><font color="#000000"></font></td>
 109 <td WIDTH="80%" BGCOLOR="#000066" NOSAVE><font color="#FFFFFF">
 110
 111 <tt> echo $GMXDATA
 112 </tt>
 113 <td></td>
 114 </tr>
 115 </table>
 116 <br>
 117 If it prints a directory name you are ready to rock, otherwise go back two steps.
 118
 119 <br><hr><br>
 120 <H2><A NAME="files">GROMACS files</A></h2>
 121 Here is an overview of the most important GROMACS file types that you will
 122 encounter during the tutorial.
 123 <DL>
 124 <DT>
 125 <h3><A NAME="top">Molecular Topology file (<TT><a href="top.html">.top</a></TT>)</A></h3>
 126 <DD>
 127 The molecular topology file is generated by the program <TT>
 128 <a href="../programs/gmx-pdb2gmx.html">gmx pdb2gmx</a></TT>.
 129 <a href="../programs/gmx-pdb2gmx.html">gmx pdb2gmx</a> translates a
 130 <a href="pdb.html">pdb</a> structure file of any peptide or protein
 131 to a molecular topology file. This topology file contains a complete
 132 description of all the interactions in your peptide or protein.
 133 <P></P>
 134
 135 <DT>
 136 <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>
 137 <DD>
 138 When the <a href="../programs/gmx-pdb2gmx.html">gmx pdb2gmx</a> program is executed
 139 to generate a molecular
 140 topology, it also translates the structure file (<TT><a href="pdb.html">.pdb</a></TT> file)
 141 to a gromos
 142 structure file (<TT><a href="gro.html">.gro</a></TT> file). The main difference between a
 143 <a href="pdb.html">pdb</a> file and a gromos file is their format and that
 144 a <TT><a href="gro.html">.gro</a></TT> file can also hold velocities. However, if you do not need the
 145 velocities, you can also use a <a href="pdb.html">pdb</a> file in all programs.
 146 To generate a box of solvent molecules
 147 around the peptide, the program
 148 <a href="../programs/gmx-solvate.html">gmx solvate</a> is used. First the program
 149 <a href="../programs/gmx-editconf.html">gmx editconf</a> should be used to
 150 define a box of appropriate size around the molecule.
 151 <a href="../programs/gmx-solvate.html">gmx solvate</a>
 152 solvates a solute molecule (the peptide) into any solvent (in this
 153 case water). The output of <TT><a href="../programs/gmx-solvate.html">gmx solvate</a></TT>
 154 is a gromos structure file of the peptide solvated in water. The
 155 <a href="../programs/gmx-solvate.html">gmx solvate</a> program also changes the
 156 molecular topology file (generated by <a href="../programs/gmx-pdb2gmx.html">gmx pdb2gmx</a>)
 157 to add solvent to the topology.
 158 <P></P>
 159
 160 <DT>
 161 <h3><A NAME="mdp">Molecular Dynamics parameter file (<TT><a href="mdp_opt.html">.mdp</a></TT>)</A></h3>
 162 <DD>
 163 The Molecular Dynamics Parameter (<TT><a href="mdp_opt.html">.mdp</a></TT>) file contains all
 164 information about the Molecular Dynamics simulation itself
 165 e.g. time-step, number of steps, temperature, pressure etc. The
 166 easiest way of handling such a file is by adapting a sample <TT><a href="mdp_opt.html">.mdp</a></TT>
 167 file. A <TT><a href="mdp.html">sample mdp file</a></TT>
 168 can be found online.
 169 <P></P>
 170
 171 <DT>
 172 <h3><A NAME="ndx">Index file (<TT><a href="ndx.html">.ndx</a></TT>)</A></h3>
 173 <DD>
 174 Sometimes you may need an index file to specify actions on groups of atoms
 175 (e.g. Temperature coupling, accelerations, freezing). Usually the default index
 176 groups will be sufficient, so for this demo we will
 177 not consider the use of index files.
 178 <P></P>
 179
 180 <DT>
 181 <h3><A NAME="tpr">Run input file (<TT><a href="tpr.html">.tpr</a></TT>)</A></h3>
 182 <DD>
 183 The next step is to combine the molecular structure (<TT><a href="gro.html">.gro</a></TT> file),
 184 topology (<TT><a href="top.html">.top</a></TT> file) MD-parameters (<TT><a href="mdp_opt.html">.mdp</a></TT> file) and
 185 (optionally) the
 186 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
 187 <TT><a href="tpb.html">.tpb</a></tt> if you don't have XDR).
 188 This file contains all information needed to start a simulation with GROMACS.
 189 The
 190 <a href="../programs/gmx-grompp.html">gmx grompp</a> program processes all
 191 input files and generates the run input
 192 <tt><a href="tpr.html">.tpr</a></tt> file.
 193 <P></P>
 194
 195 <DT>
 196 <h3><A NAME="trx">Trajectory file (<TT><a href="trr.html">.trr</a></TT></A>)</h3>
 197 <DD>
 198 Once the run input file is available, we can start the
 199 simulation. The program which starts the simulation is called
 200 <a href="../programs/gmx-mdrun.html">gmx mdrun</a>. The only input file
 201 of <TT><a href="../programs/gmx-mdrun.html">gmx mdrun</a></TT> you usually need
 202 to start a run
 203 is the run input file (<TT><a href="tpr.html">.tpr</a></TT> file).
 204 The output files of
 205 <TT><a href="../programs/gmx-mdrun.html">gmx mdrun</a></TT> are the
 206 trajectory file (<TT><a href="trr.html">.trr</a></TT> file
 207 or <TT><a href="trj.html">.trj</a></TT> if you don't have XDR) and a logfile (
 208 <TT><a href="log.html">.log</A></TT> file).
 209 <P></P>
 210
 211 </DL>
 212
 213 <br><hr><br>
 214
 215 <P><H2><A NAME="ref">References</A></h2>
 216
 217 <blockquote>
 218 <dl>
 219
 220 <dt><A NAME="berendsen81">Berendsen, H.J.C., Postma, J.P.M., van
 221 Gunsteren, W.F., Hermans, J. (1981) <dd><it>Intermolecular
 222 Forces</it>, chapter Interaction models for water in relation to
 223 protein hydration, pp 331-342. Dordrecht: D. Reidel Publishing Company
 224 Dordrecht</dd><p>
 225
 226 <dt><A NAME="kabsch83">Kabsch, W., Sander, C. (1983). <dd>Dictionary
 227 of protein secondary structure: Pattern recognition of hydrogen-bonded
 228 and geometrical features. <it>Biopolymers</it> <b>22</b>,
 229 2577--2637.</dd><p>
 230
 231 <dt><A NAME="mierke91">Mierke, D.F., Kessler, H. (1991). <dd>Molecular
 232 dynamics with dimethyl sulfoxide as a solvent. Conformation of a
 233 cyclic hexapeptide. <it>J. Am. Chem. Soc.</it> <b>113</b>, 9446.</dd><p>
 234
 235 <dt><A NAME="stryer88">Stryer, L. (1988). <dd><it>Biochemistry</it>
 236 vol. 1, p. 211. New York: Freeman, 3 edition.</dd><p>
 237
 238 </dl>
 239 </blockquote>