3 <TITLE>Getting started - Methanol
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11 <td ALIGN=LEFT VALIGN=TOP WIDTH=
280><br><h2>Getting started - Methanol
</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>
17 <P><H2>Methanol
</A></H2>
18 Now you are going to simulate
216 molecules of methanol
19 in a cubic box. In this example the GROMACS
20 software team already generated most of the neccesary input
21 files. The files needed in this example are:
23 <LI> Initial structure of a box of
216 methanol molecules (
<TT><a href=
"gro.html">.gro
</a></TT>)
</li>
25 <LI> Topology file of methanol (
<tt><a href=
"top.html">.top
</a></tt>)
</li>
26 <LI> Molecular Dynamics parameter file (
<TT><a href=
"mdp_opt.html">.mdp
</a></TT>)
</li>
29 Change your directory to
<tt>tutor/methanol
</tt>:
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36 <tt> cd tutor/methanol
</tt>
41 Let's first have a look at the coordinate file:
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54 Or to view the methanol box graphically:
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61 <tt> rasmol methanol.pdb
67 The Carbon group (CH3) is treated as one particle. In the file it
68 is called Me1 (methyl
1) and rasmol does not recognize it as carbon (and hence
73 Since all the neccesary files are available, we are going to
74 preprocess the input files to create a run input
75 (
<TT><a href=
"tpr.html">.tpr
</a></TT>) file.
76 This run input file is the only input file for the
77 MD-program
<TT><a href=
"mdrun.html">mdrun
</a></TT>.
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91 Now it's time to start the simulation of
20 picoseconds.
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105 After the MD simulation is finished, it is possible to view the
106 trajectory with the
<a href=
"ngmx.html">ngmx
</a> program:
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121 When the program starts, you must select a group of atoms to view. In
122 our case that will be
"MeOH" (for methanol) or
"System", which is the
123 same for a box of methanol as we have. Select one and click OK. Then
124 select Display-
>Animate from the menu. Use the buttons to see your
125 methanol moving (note:
"Play" steps one frame forward;
"Fast Forward"
126 plays;
"Rewind" skips back to the beginning of the trajectory).
130 <h2>Analysis of the simulation
</h2>
132 <li><p> Calculate a radial distribution function of the oxygen atoms
133 around oxygen atoms. The index file
<TT><a
134 href=
"ndx.html">index.ndx
</a></TT> now contains two groups, one with
135 the methyl atoms and one with the oxygen atoms.
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142 <tt> g_rdf -n index -o rdf-oo.xvg
148 The program will ask you for how many groups you want the calculate
149 the RDF, answer
1 (and select oxygen and oxygen). Now,
150 view the output graph.
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157 <tt> xmgrace rdf-oo.xvg
163 Which shows you the radial distribution function for oxygen-oxygen in
164 Methanol. Now do the same thing using the methyl group as reference and
165 as target (and use e.g.
<tt>rdf-mm.xvg
</tt> as output file name). View all
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173 <tt> xmgrace rdf-oo.xvg rdf-mm.xvg ../water/rdf.xvg -legend load
179 The
<tt>xmgrace
</tt> program will display three different graphs.
180 <font color=
"red">Compare the resulting graphs. Explain the differences and the
186 We can also do a direct analysis of the number of hydrogen bonds in
187 methanol, based on O-O distance and O-H ... O angle.
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200 Select twice
0, when asked. Check the output with
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207 <tt> xmgrace hbnum.xvg
213 <font color=
"red">What is the number of hydrogen bonds per methanol
214 molecule? What is the maximum possible number? Compare the results to
215 those from water
</font>
218 <li><p> As a further test of the simulation we will compute the self
219 diffusion constant of Methanol, again from the
<b>Mean
220 square displacement
</b> (MSD) function.
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233 (Select Me1, or O2). View the output
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246 Check that the graph is roughly linear. The
<tt>g_msd
</tt> program also
247 computes the diffusion constant D for you.
248 <font color=
"red">Compare the result to water. Is it as you would expect?
254 <a href=
"mixed.html"><h3>Go to the next step
</h3></a>