[gmx-users] radial distribution function

[Tsjerk Wassenaar]

Hey,

This is just exactly what you'd expect for polymer chains in a
solution (suspension?). From the closest neighbours the fine
structure, the discrete distribution of carbon atoms, is still seen,
but for those further away it's blurred. Dallas' excercise should be a
fine way to show that more explicitly.

Cheers,

Tsjerk

On Fri, Sep 16, 2011 at 12:26 AM, Dallas Warren
<Dallas.Warren at monash.edu> wrote:
> Load up some frames into VMD and start measuring the distances shown by the
> peaks in your RDF, link them with what you actually see in there (using
> something like a transparent representation of the carbon atom(s) using VDW
> then set the sphere scale so that it matches the correct radius, may be an
> easier way to do this, but this would make it easy to see).  Appears it may
> be something real, so just check the coordinate file and see where they are
> actually coming from.
>
>
>
> Catch ya,
>
> Dr. Dallas Warren
>
> Medicinal Chemistry and Drug Action
>
> Monash Institute of Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3010
> dallas.warren at monash.edu
>
> +61 3 9903 9304
> ---------------------------------
> When the only tool you own is a hammer, every problem begins to resemble a
> nail.
>
>
>
> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
> On Behalf Of Moeed
> Sent: Friday, 16 September 2011 12:55 AM
> To: jalemkul at vt.edu; Discussion list for GROMACS users
> Subject: Re: [gmx-users] radial distribution function
>
>
>
> Hello again,
>
> I tried comparing RDF plots generated by sampling from 4 to 5 ns run and a
> longer run from 4 to 30 ns to see whether the small jumps on the plot are
> due to insufficient sampling. Attached is the new plot showing that two RDF
> curves are almost identical. I only wanted to let you know and please
> comment on the attached plot if you have any ideas. Thank you. :)
>
> Moeed
>
> On Sat, Sep 10, 2011 at 10:00 AM, Moeed <lecielll at googlemail.com> wrote:
>
> Thank you for your input. I am going to run for another 15 ns to see if the
> little jumps vanish.
>
> Best,
>
>
>
> On Fri, Sep 9, 2011 at 9:16 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
> lina wrote:
>
>
>
> On Sat, Sep 10, 2011 at 3:35 AM, Moeed <lecielll at googlemail.com
> <mailto:lecielll at googlemail.com>> wrote:
>
>    Dear users,
>
>    I have created radial distribution function plot for Carbon atoms in
>    a system containing polymer chains. I see some little jumps between
>    first and second peak.
>    I need your help to comment on how this behavior can be justified
>    (or if the plot is wrong).
>
>    g_rdf -f *.trr -s *.tpr -o *.xvg -n *.ndx –b xxx
>    Thank you in advance.
>
>
> I think your figure is fine.
>
>
>
> I think, based on information given in subsequent messages, that there is
> insufficient data collection to assess whether this RDF plot is as
> meaningful as it could be.  There is nothing glaringly wrong, but the
> roughness is due to insufficient sampling.
>
>
>
> You just need how to proper interpret your figures, truly understand what
> the "radial distribution" means.
>
>
>
>
> I think it inappropriate to suggest that the OP does not understand the
> concept behind the figure; some guidance, perhaps is necessary, but nothing
> more.
>
> -Justin
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands