[gmx-users] radial distribution function

[Moeed]

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 <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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