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On 12/26/2011 7:53 PM, mohammad agha wrote:
<blockquote
cite="mid:1324889604.84082.YahooMailNeo@web125703.mail.ne1.yahoo.com"
type="cite">
<div style="color: rgb(0, 0, 0); background-color: rgb(255, 255,
255); font-family: verdana,helvetica,sans-serif; font-size:
12pt;">
<div>Dear Prof.</div>
<div><br>
</div>
<div>I have several questions about trjconv, please help me.</div>
<div><br>
</div>
<div>In my simulation is created 2 micelles.</div>
<div>1- When I do 3 steps of micelle clustering as follows:</div>
<div><br>
</div>
<div> a- <code>trjconv <span style="background-color:
rgb(255, 255, 0);">-f md.xtc</span> -o a_cluster.gro<span
style="background-color: rgb(255, 255, 0);"> -e 600000 </span>-pbc
cluster</code></div>
<div><code> b- </code><code>grompp <span
style="background-color: rgb(255, 255, 0);">-f md.mdp</span>
-c a_cluster.gro -o a_cluster.tpr</code></div>
<div><code> c- </code><code>trjconv <span
style="background-color: rgb(255, 255, 0);">-f </span><span
style="background-color: rgb(255, 255, 0);">md.xtc</span>
-o a_cluster.xtc -s a_cluster.tpr -pbc nojump</code></div>
<div><br>
<code></code></div>
<div>I view 2 micelles according to result of my simulation in
VMD but in ngmx isn't view 2 micelles but just is view 1
micelle and reminder of monomers are collected in several
groups in different places.</div>
</div>
</blockquote>
<br>
So you don't have a single cluster of atoms... so as trjconv -h
notes, using -pbc cluster isn't very useful when you don't have a
cluster of atoms. All my advice of two days ago on this point still
applies.<br>
<br>
<blockquote
cite="mid:1324889604.84082.YahooMailNeo@web125703.mail.ne1.yahoo.com"
type="cite">
<div style="color: rgb(0, 0, 0); background-color: rgb(255, 255,
255); font-family: verdana,helvetica,sans-serif; font-size:
12pt;">
<div>Is it right if my criterion be view in VMD and is my
micelle clustering correct?<br>
</div>
</div>
</blockquote>
<br>
It's "correct" if it looks the way you want it to.<br>
<br>
<blockquote
cite="mid:1324889604.84082.YahooMailNeo@web125703.mail.ne1.yahoo.com"
type="cite">
<div style="color: rgb(0, 0, 0); background-color: rgb(255, 255,
255); font-family: verdana,helvetica,sans-serif; font-size:
12pt;">
<div><code></code></div>
<div><br>
</div>
<div>2- If I select surfactants for clustering group and system
for output group in step (a) and I select system for output
group in step (c), command g_clustsize doesn't work correct,
consequently, I did under step and made a .xtc file only for
surfactants: <br>
</div>
<div> <br>
</div>
<div> i- <span class="tab">trjconv -f md.trr -o
md-surfactant.xtc -n index.ndx<br>
</span></div>
<div> <br>
</div>
<div>Then I did steps a, b and c for md-surfactant.xtc and in
all of steps I selected surfactants for clustering and output
group. Next, I did g_clustsize and it answered me correct. <br>
</div>
<div>May I know that my way is correct, please?<br>
</div>
<div><br>
</div>
<div>3- By upper way I have 2 micelles that I got index.ndx file
for cluster with maximum size by g_clustsize (maxcluster.ndx).</div>
<div>May I know how can I use from this for next calculation if
I want consider only maximum cluster with all of system (water
and ion) in calculations (for example rdf, gyration and etc)?<br>
</div>
</div>
</blockquote>
<br>
Again I think you are not using the word cluster in the sense the
GROMACS tools are. Each micelle could be a cluster of atoms, or the
pair of micelles could be a cluster of micelles. How to use the
tools will differ according to what you are trying to calculate on
what kind of cluster. Anyway, the atom numbers do not change with
the configuration of the atoms, so the same index file group
identifies the surfactant atoms in each frame. To identify the
*time* of the configuration with the largest diameter, something
like g_mindist -max might serve. However you may need to resolve
your PBC issue first.<br>
<br>
Mark<br>
<br />--
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