<p style="border:0; padding:0; margin:0; font-family:'Gulim'; font-size:10pt; cursor: text;"><p style="font-family: Gulim; font-size: 10pt; border: 0px; padding: 0px; margin: 0px; cursor: text;">Hi Andre, </p><p style="font-family: Gulim; font-size: 10pt; border: 0px; padding: 0px; margin: 0px; cursor: text;"><br></p><p style="font-family: Gulim; font-size: 10pt; border: 0px; padding: 0px; margin: 0px; cursor: text;">Thank you for your input.</p><p style="font-family: Gulim; font-size: 10pt; border: 0px; padding: 0px; margin: 0px; cursor: text;"><br></p><p style="font-family: Gulim; font-size: 10pt; border: 0px; padding: 0px; margin: 0px; cursor: text;"><br></p><blockquote style="font-family: Gulim; font-size: 12px; border-left-style: solid; border-left-width: 2px; margin: 0pt 0pt 0pt 0.8em; padding-left: 1em;"><div style="font-family:arial,돋움;line-height:1.5"><b>보낸사람</b> : "André Farias de Moura" <moura@ufscar.br><br><b>받는사람</b> : Discussion list for GROMACS us <gmx-users@gromacs.org><br><b>받은날짜</b> : 2015년 1월 8일(목) 22:05:39<br><b>제목</b> : Re: [gmx-users] RDF plot with large g(r) values<br><!-- original content --><div style="margin-top:5px;"><pre>RDF values are sensitive to the volume of the system, so if you put the
same solutes inside a larger/smaller box, RDF values change accordingly
(check basic definitions of RDF in simulation handbooks to make sure you
understand this relation).</pre></div></div></blockquote><font face="monospace"><span style="font-size: 12px; line-height: 18px; white-space: pre;">Ah right, that explains why my RDF values dropped if I put a larger amount of water in the same box.<br></span></font><blockquote style="font-family: Gulim; font-size: 12px; border-left-style: solid; border-left-width: 2px; margin: 0pt 0pt 0pt 0.8em; padding-left: 1em;"><div style="font-family:arial,돋움;line-height:1.5"><div style="margin-top:5px;"><pre>
and even if you have the same size and composition, RDF may become really
large if molecules aggregate.</pre></div></div></blockquote><font face="monospace"><span style="font-size: 12px; line-height: 18px; white-space: pre;">Yep, I have a droplet where the Na+ and OH- ions tend to aggregate within the solution, the high g(r) peak in the RDF almost doubles the other systems with no aggregation.<br></span>In this case, can I still use my RDF plots?<br><br>Regards,<br>Kester<br><span style="font-size: 12px; line-height: 18px; white-space: pre;"><br></span></font><blockquote style="font-family: Gulim; font-size: 12px; border-left-style: solid; border-left-width: 2px; margin: 0pt 0pt 0pt 0.8em; padding-left: 1em;"><div style="font-family:arial,돋움;line-height:1.5"><div style="margin-top:5px;"><pre>
On Thu, Jan 8, 2015 at 7:48 AM, Kester Wong <kester2014@ibs.re.kr> wrote:
> Dear all,
>
>
>
> My apologies if this question sounds too basic of if it has been covered.
>
> I did some RDF calculations, and as when I plotted the figures, the g(r)
> values are in the hundreds, whereas the papers that I have seen are all in
> the range of 0-12.
>
> The x-axis (nm), however, seemed to be correct.
>
>
>
> Regards,
>
> Kester
>
>
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--
_____________
Prof. Dr. André Farias de Moura
Department of Chemistry
Federal University of São Carlos
São Carlos - Brazil
phone: +55-16-3351-8090
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</kester2014@ibs.re.kr></pre></div><!-- original content --><br></div></blockquote></p>
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