[gmx-users] radial distribution function

[Moeed]

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 <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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
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