[gmx-users] RDF plot with large g(r) values

[André Farias de Moura]

makes sense now, your system is quite heterogeneous.

you may use your RDF but some reviewers might not agree with this kind of
analysis for heterogeneous systems, so you have to explain why your
correlation peaks are so high and why the profiles don't converge to unity.

On Fri, Jan 9, 2015 at 12:34 AM, Kester Wong <Kester2014 at ibs.re.kr> wrote:

> Hi Andre,
>
>
> Thank you for your input.
>
>
>
> *보낸사람* : "André Farias de Moura" <moura at ufscar.br>
> *받는사람* : Discussion list for GROMACS us <gmx-users at gromacs.org>
> *받은날짜* : 2015년 1월 8일(목) 22:05:39
> *제목* : Re: [gmx-users] RDF plot with large g(r) values
>
> 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).
>
> Ah right, that explains why my RDF values dropped if I put a larger amount
> of water in the same box.
>
>
> and even if you have the same size and composition, RDF may become really
> large if molecules aggregate.
>
> 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.
> In this case, can I still use my RDF plots?
>
> Regards,
> Kester
>
>
> On Thu, Jan 8, 2015 at 7:48 AM, Kester Wong  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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-- 
_____________

Prof. Dr. André Farias de Moura
Department of Chemistry
Federal University of São Carlos
São Carlos - Brazil
phone: +55-16-3351-8090