[gmx-users] g_rdf

[Justin Lemkul]

On 10/31/12 4:56 PM, Ali Alizadeh wrote:
> Dear All users
>
> I have a system that contains water , methane and propane in 240 k and 300
> bar,
>
> My simulation box is rectangular .
>
> Water film is in middle of my box. Methane and propane is around it.
>
> My simulation box is symmetric,
>
> 1- I used g_rdf program for . My result is exotic. My g(r) in profile do
> not reach to 1 . Why ?
>

"Exotic" is not a useful description.  Are there systematic trends?  Bumps in 
the plot? What's going on?  What groups are you choosing for the analysis?  It 
seems to me the asymmetry in the system will cause some odd behavior in an RDF, 
but without seeing an actual plot (i.e. a picture) then it's hard to comment.

>
> 2- I test my number density profiles(from g_density) but they do not
> correct result because when i
>
> calculate number of my molecules by multiplying volume to average number
> density, i can not take the same number of my particle,
>

 From the extensive posts on this topic in recent days, you should know that 
there are issues with g_density.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
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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