Hello Aneesh,
Just to check, have you look at your system after you have applied the
center/image commands (i.e. put a trajout command after the center and image
commands and check the output trajectory) to visually make sure the RDF you
are getting makes sense? Sometimes the image command doesn't work exactly
the way you think it might.
-Dan
On Sat, Apr 3, 2010 at 12:49 AM, aneesh cna <aneeshcna.gmail.com> wrote:
> Dear Amber users,
>
> I am using Ptraj in Amber 9.0 for RDF ( Radial
> distribution function) calculation. My simulation system contains reverse
> micelle and I am calculating the site-site radial distribution of organic
> molecules ( that form the core of the reverse micelle) around the
> surfactant head group ( that form the corona of the reverse micelle).
> Given below is the Ptraj input for RDF calculation...
>
>
> ************************************************************
> trajin md.crd
>
>
> center :MOL mass origin
> image origin center familiar
> center :SUR mass origin
> image origin center familiar # here I am wrapping the
> reverse
> micelle into the unit cell ( because I ran system with ' iwrap = 1' )
>
>
> radial H_O1 0.05 20.0 :SUR.H6 :MOL.O1
> radial H_O2 0.05 20.0 :SUR.H6 :MOL.O2
>
> ***********************************************************************************************
>
>
> Every thing went fine, but what I am worried about is the maximum value
> for
> g(r) ( maximum value going up to ~80). I browsed through Internet, but
> can't able find out any RDF plot with g(r) goes to maximum value like what
> I
> have in my case. As a test run , I calculate water RDF and that went fine.
> Am I doing some mistake with calculation? Is it OK with what value I am
> getting for g(r)?.
>
>
> I have attached a RDF plot for your quick reference. Waiting for your
> valuable reply
>
>
> Thanks in advance
>
>
> Sincerely
> Aneesh
>
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>
>
--
-------------------------
Daniel R. Roe
Postdoctoral Associate
SAS - Chemistry & Chemical Biology
610 Taylor Road
Piscataway, NJ 08854
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Received on Mon Apr 05 2010 - 05:30:02 PDT
