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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">I don’t do COM calculations, so don’t know directly, but have a read of “g_rdf –h”, method is outlined there and I suspect there are a number of discussions
on it within the emailing list archive that you should search.<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"><b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> mohammad agha [mailto:mra_bu@yahoo.com]
<br>
<b>Sent:</b> Tuesday, 22 November 2011 4:28 AM<br>
<b>To:</b> Dallas Warren<br>
<b>Subject:</b> Re: [gmx-users] density<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span class="yshortcuts"><span style="font-size:10.0pt;font-family:"Verdana","sans-serif";color:#1F497D">Dear Prof. Warren</span></span><span style="font-family:"Verdana","sans-serif";color:black"><o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-family:"Verdana","sans-serif";color:black">Excuse me, may I know that how to obtain the average radial density functions relative to the center of mass with g_rdf?<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-family:"Verdana","sans-serif";color:black">I think these plots are produced by counting the number of selected atoms that are within the x angstrom wide shells around the micelle COM, and I think
that I should use from : <b><i>N= 4 π ρ∫ <sub>0</sub> <sup>00</sup> r<sup>2</sup> g(r) dr.
</i></b>, but I don't know how to find N and what is the computation carefully?<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-family:"Verdana","sans-serif";color:black">Please help me.<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-family:"Verdana","sans-serif";color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-family:"Verdana","sans-serif";color:black">Best Regards<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-family:"Verdana","sans-serif";color:black">Sara<o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt;background:white"><b><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:black">From:</span></b><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:black"> Dallas Warren <<a href="mailto:Dallas.Warren@monash.edu">Dallas.Warren@monash.edu</a>><br>
<b>To:</b> mohammad agha <<a href="mailto:mra_bu@yahoo.com">mra_bu@yahoo.com</a>>; Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>>
<br>
<b>Sent:</b> Monday, November 21, 2011 2:04 AM<br>
<b>Subject:</b> RE: [gmx-users] density</span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:11.0pt;color:#1F497D">Last bit here, that is probably done using a RDF, which is a probability function, which you can then convert into a number of atoms in each shell.</span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:11.0pt;color:#1F497D"> </span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:10.0pt;color:#1F497D">Catch ya,<br>
<br>
Dr. Dallas Warren</span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:10.0pt;color:#1F497D">Medicinal Chemistry and Drug Action</span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:10.0pt;color:#1F497D">Monash Institute of Pharmaceutical Sciences, Monash University<br>
381 Royal Parade, Parkville VIC 3010<br>
<a href="mailto:dallas.warren@monash.edu">dallas.warren@monash.edu</a></span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:10.0pt;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;color:#1F497D">
</span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:11.0pt;color:#1F497D"> </span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><b><span style="font-size:10.0pt;color:black">From:</span></b><span style="font-size:10.0pt;color:black">
<a href="mailto:gmx-users-bounces@gromacs.org">gmx-users-bounces@gromacs.org</a> [<a href="mailto:gmx-users-bounces@gromacs.org">mailto:gmx-users-bounces@gromacs.org</a>]
<b>On Behalf Of </b>mohammad agha<br>
<b>Sent:</b> Sunday, 20 November 2011 5:52 PM<br>
<b>To:</b> <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
<b>Subject:</b> [gmx-users] density</span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="color:black"> <o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="color:black">Dear Prof.
<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="color:black"> <o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="color:black">I have problems about density. I equilibrated my system consist 500 surfactants and 60000 water molecules in martini coarse-grained for 120 ns and my results of g_energy next pr.mdp for
density are:<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="color:black"> <o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="color:black">average = 907.701<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="color:black">err.est = 0.61<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="color:black">rmsd = 2.54989<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="color:black">tot-drift = -3.4173<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="color:black"> <o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="color:black">I don't know about good quantity of err.est, rmsd and tot-drift for density adjustment? and when my system has been equilibrated?<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="color:black">May I know about my problem, please?<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="color:black"> <o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="color:black">On the other hand, "density distribution for different groups of the system in terms of their distance from micell's COM distance" is considered In the articles about surfactants. I think
that it is possible with g_density but this program compute the density as the function of box(nm). May I know about this problem, Please?<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="color:black"> <o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="color:black">Best Regards<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="color:black">sara<o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt;background:white"><span style="color:black"><o:p> </o:p></span></p>
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