<html><body><div style="color:#000; background-color:#fff; font-family:verdana, helvetica, sans-serif;font-size:12pt"><div><span>Dear Prof.</span></div><div><br><span></span></div><div><span>Thank you very much for your reply.</span></div><div><span>Excuse me, I saw a figure in one article that showed the number density distribution for the surfactant molecules' angles for the production run. how? Is this as same as number density for coordinate number?how?</span></div><div><span>And some of articles with gromacs have a figure of radial density and radial number density and density as r(distance), I think those have been obtained with g_rdf, but how as a figure? <br></span></div><div>Please help me.</div><div><br></div><div>Best Regards</div><div>Sara<br></div> <div style="font-family: verdana, helvetica, sans-serif; font-size: 12pt;"> <div style="font-family: times new roman, new york, times, serif; font-size: 12pt;"> <font face="Arial" size="2">
<hr size="1"> <b><span style="font-weight:bold;">From:</span></b> Dallas Warren <Dallas.Warren@monash.edu><br> <b><span style="font-weight: bold;">To:</span></b> Discussion list for GROMACS users <gmx-users@gromacs.org> <br> <b><span style="font-weight: bold;">Sent:</span></b> Monday, December 12, 2011 12:38 AM<br> <b><span style="font-weight: bold;">Subject:</span></b> RE: [gmx-users] coordinate number aroud the first shell<br> </font> <br>
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<div class="yiv1323855501MsoNormal"><span style="font-size:11.0pt;color:#1F497D;">1 – number of atoms divided by size of the box.</span></div>
<div class="yiv1323855501MsoNormal"><span style="font-size:11.0pt;color:#1F497D;">2 – manually or via a script. I have a script set up within Sigma Plot that I use for mine, but can be done in any other spreadsheet and programming language
too.</span></div>
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<div class="yiv1323855501MsoNormal"><span style="font-size:10.0pt;color:#1F497D;">Catch ya,<br>
<br>
Dr. Dallas Warren</span></div>
<div class="yiv1323855501MsoNormal"><span style="font-size:10.0pt;color:#1F497D;">Medicinal Chemistry and Drug Action</span></div>
<div class="yiv1323855501MsoNormal"><span style="font-size:10.0pt;color:#1F497D;">Monash Institute of Pharmaceutical Sciences</span><span style="font-size:10.0pt;color:#1F497D;">, Monash University<br>
381 Royal Parade, Parkville VIC 3010<br>
dallas.warren@monash.edu</span></div>
<div class="yiv1323855501MsoNormal"><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;">
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<div class="yiv1323855501MsoNormal"><b><span style="font-size:10.0pt;">From:</span></b><span style="font-size:10.0pt;"> gmx-users-bounces@gromacs.org [mailto:gmx-users-bounces@gromacs.org]
<b>On Behalf Of </b>mohammad agha<br>
<b>Sent:</b> Sunday, 11 December 2011 11:15 PM<br>
<b>To:</b> gmx-users@gromacs.org<br>
<b>Subject:</b> [gmx-users] coordinate number aroud the first shell</span></div>
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<div class="yiv1323855501MsoNormal" style="background:white;"><span style="color:black;">Dear Prof.</span></div>
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<div class="yiv1323855501MsoNormal" style="background:white;"><span style="color:black;"> </span></div>
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<div class="yiv1323855501MsoNormal" style="background:white;"><span style="color:black;">I want to obtain the coordinate number from the first shell around my cluster, I want to use from integration of the 4*pi*(number density)*area(g(r)r2dr)
until the first minimum of the RDF, but I have some questions: Please help me</span></div>
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<div class="yiv1323855501MsoNormal" style="background:white;"><span style="color:black;">1- How do I obtain the number density for special rdf? by g_density? how?</span></div>
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<div class="yiv1323855501MsoNormal" style="background:white;"><span style="color:black;">2- After this, should I compute N (coordinate number) manually?</span></div>
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<div class="yiv1323855501MsoNormal" style="background:white;"><span style="color:black;"> </span></div>
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<div class="yiv1323855501MsoNormal" style="background:white;"><span style="color:black;">Best Regards</span></div>
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<div class="yiv1323855501MsoNormal" style="background:white;"><span style="color:black;">Sara</span></div>
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