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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Additionally, you need to be careful with the PBC when using g_gyrate, as if part of the micelle is split across it, then the radius provided will be wrong.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">If you have 3 micelles, then you will have to generate an index file with a group for the molecules/atoms within each of the micelles, then pass each group
to g_gyrate separately to get the radius for each micelle.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">From what you have written you have calculated the radius of gyration of all of the surfactant molecules within your simulation, which is more than likely not
what you want.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Catch ya,<br>
<br>
Dr. Dallas Warren<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Medicinal Chemistry and Drug Action<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Monash Institute of Pharmaceutical Sciences</span><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D">, Monash University<br>
381 Royal Parade, Parkville VIC 3010<br>
dallas.warren@monash.edu<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D">+61 3 9903 9304<br>
---------------------------------<br>
When the only tool you own is a hammer, every problem begins to resemble a nail.</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">
<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:windowtext">From:</span></b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:windowtext"> gmx-users-bounces@gromacs.org [mailto:gmx-users-bounces@gromacs.org]
<b>On Behalf Of </b>Mark Abraham<br>
<b>Sent:</b> Wednesday, 11 April 2012 5:05 PM<br>
<b>To:</b> Discussion list for GROMACS users<br>
<b>Subject:</b> Re: [gmx-users] regarding micelle and its analysis<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">On 11/04/2012 3:48 PM, priya thiyagarajan wrote: <o:p></o:p></p>
<p class="MsoNormal">hello sir,<br>
<br>
i am studying about micelle formation of surfactants. i performed my run for 10ns.. when i visualize my final md pdb file i got around 2 to 3 micelles.
<br>
<br>
my doubt is while performing analysis , g_gyrate giving a value of around 3nm..<br>
<br>
this value corresponds to which micelle..<o:p></o:p></p>
<p class="MsoNormal"><br>
None of them. It corresponds to the group you told g_gyrate to analyse. See g_gyrate -h. Since you haven't told us which group you told g_gyrate to use, you've forced me to guess that you told it to work on all your surfactant molecules. If you'd given a full
description of what you'd done, then you'd be more likely to have people wanting and able to help you, and thus be more likely to get useful help. Anyway, g_gyrate can't guess that you want it to look at some magic subsets of the whole system. You have to
define the subsets, e.g. with g_select, and only then can g_gyrate compute properties on them.<br>
<br>
Mark<br>
<br>
<br>
<o:p></o:p></p>
<p class="MsoNormal"><br>
how its calculating this value.. <br>
<br>
please help me with your answer..<br>
<br>
i am so confused with my analysis..<br>
<br>
thanking you,<br>
<br>
<br>
<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
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