<html><body><div style="color:#000; background-color:#fff; font-family:verdana, helvetica, sans-serif;font-size:12pt"><div><span>Thanks Prof. Warren</span></div><div><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> Tuesday, November 22, 2011 12:23 AM<br> <b><span style="font-weight: bold;">Subject:</span></b> RE: [gmx-users] density<br> </font> <br>
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<div class="yiv1379843094MsoNormal"><span style="font-size:11.0pt;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.</span></div>
<div class="yiv1379843094MsoNormal"><span style="font-size:11.0pt;color:#1F497D;"> </span></div>
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<div class="yiv1379843094MsoNormal"><span style="font-size:10.0pt;color:#1F497D;">Catch ya,<br>
<br>
Dr. Dallas Warren</span></div>
<div class="yiv1379843094MsoNormal"><span style="font-size:10.0pt;color:#1F497D;">Medicinal Chemistry and Drug Action</span></div>
<div class="yiv1379843094MsoNormal"><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="yiv1379843094MsoNormal"><span style="font-size:10.0pt;color:#1F497D;">+61 3 9903 9304<br>
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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></div>
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<div class="yiv1379843094MsoNormal"><b><span style="font-size:10.0pt;">From:</span></b><span style="font-size:10.0pt;"> 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</span></div>
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<div class="yiv1379843094MsoNormal" style="background:white;"><span class="yiv1379843094yshortcuts"><span style="font-size:10.0pt;color:#1F497D;">Dear Prof. Warren</span></span><span style="color:black;"></span></div>
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<div class="yiv1379843094MsoNormal" style="background:white;"><span style="color:black;"> </span></div>
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<div class="yiv1379843094MsoNormal" style="background:white;"><span style="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?</span></div>
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<div class="yiv1379843094MsoNormal" style="background:white;"><span style="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?</span></div>
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<div class="yiv1379843094MsoNormal" style="background:white;"><span style="color:black;">Please help me.</span></div>
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<div class="yiv1379843094MsoNormal" style="background:white;"><span style="color:black;"> </span></div>
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<div class="yiv1379843094MsoNormal" style="background:white;"><span style="color:black;">Best Regards</span></div>
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<div class="yiv1379843094MsoNormal" style="background:white;"><span style="color:black;">Sara</span></div>
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<span style="font-size:10.0pt;color:black;">
<hr align="center" size="1" width="100%">
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<div class="yiv1379843094MsoNormal" style="margin-bottom:12.0pt;background:white;"><b><span style="font-size:10.0pt;color:black;">From:</span></b><span style="font-size:10.0pt;color:black;"> Dallas Warren <<a rel="nofollow" ymailto="mailto:Dallas.Warren@monash.edu" target="_blank" href="mailto:Dallas.Warren@monash.edu">Dallas.Warren@monash.edu</a>><br>
<b>To:</b> mohammad agha <<a rel="nofollow" ymailto="mailto:mra_bu@yahoo.com" target="_blank" href="mailto:mra_bu@yahoo.com">mra_bu@yahoo.com</a>>; Discussion list for GROMACS users <<a rel="nofollow" ymailto="mailto:gmx-users@gromacs.org" target="_blank" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>>
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<b>Sent:</b> Monday, November 21, 2011 2:04 AM<br>
<b>Subject:</b> RE: [gmx-users] density</span><span style="color:black;"></span></div>
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<div class="yiv1379843094MsoNormal" 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;"></span></div>
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<div class="yiv1379843094MsoNormal" style="background:white;"><span style="font-size:11.0pt;color:#1F497D;"> </span><span style="color:black;"></span></div>
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<div class="yiv1379843094MsoNormal" style="background:white;"><span style="font-size:10.0pt;color:#1F497D;">Catch ya,<br>
<br>
Dr. Dallas Warren</span><span style="color:black;"></span></div>
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<div class="yiv1379843094MsoNormal" style="background:white;"><span style="font-size:10.0pt;color:#1F497D;">Medicinal Chemistry and Drug Action</span><span style="color:black;"></span></div>
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<div class="yiv1379843094MsoNormal" 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 rel="nofollow" ymailto="mailto:dallas.warren@monash.edu" target="_blank" href="mailto:dallas.warren@monash.edu">dallas.warren@monash.edu</a></span><span style="color:black;"></span></div>
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<div class="yiv1379843094MsoNormal" 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;"></span></div>
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<div class="yiv1379843094MsoNormal" style="background:white;"><span style="font-size:11.0pt;color:#1F497D;"> </span><span style="color:black;"></span></div>
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<div class="yiv1379843094MsoNormal" style="background:white;"><b><span style="font-size:10.0pt;color:black;">From:</span></b><span style="font-size:10.0pt;color:black;">
<a rel="nofollow" ymailto="mailto:gmx-users-bounces@gromacs.org" target="_blank" href="mailto:gmx-users-bounces@gromacs.org">gmx-users-bounces@gromacs.org</a> [<a rel="nofollow" ymailto="mailto:gmx-users-bounces@gromacs.org" target="_blank" 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 rel="nofollow" ymailto="mailto:gmx-users@gromacs.org" target="_blank" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
<b>Subject:</b> [gmx-users] density</span><span style="color:black;"></span></div>
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<div class="yiv1379843094MsoNormal" style="background:white;"><span style="color:black;">Dear Prof.
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<div class="yiv1379843094MsoNormal" style="background:white;"><span style="color:black;"> </span></div>
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<div class="yiv1379843094MsoNormal" 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:</span></div>
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<div class="yiv1379843094MsoNormal" style="background:white;"><span style="color:black;"> </span></div>
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<div class="yiv1379843094MsoNormal" style="background:white;"><span style="color:black;">average = 907.701</span></div>
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<div class="yiv1379843094MsoNormal" style="background:white;"><span style="color:black;">err.est = 0.61</span></div>
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<div class="yiv1379843094MsoNormal" style="background:white;"><span style="color:black;">rmsd = 2.54989</span></div>
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<div class="yiv1379843094MsoNormal" style="background:white;"><span style="color:black;">tot-drift = -3.4173</span></div>
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<div class="yiv1379843094MsoNormal" 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?</span></div>
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<div class="yiv1379843094MsoNormal" style="background:white;"><span style="color:black;">May I know about my problem, please?</span></div>
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<div class="yiv1379843094MsoNormal" 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?</span></div>
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<div class="yiv1379843094MsoNormal" style="background:white;"><span style="color:black;"> </span></div>
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<div class="yiv1379843094MsoNormal" style="background:white;"><span style="color:black;">Best Regards</span></div>
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<div class="yiv1379843094MsoNormal" style="background:white;"><span style="color:black;">sara</span></div>
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