AMBER Archive (2009)

Subject: Re: [AMBER] ptraj-radial distribution function

From: Christof Jaeger (christof.jaeger_at_chemie.uni-erlangen.de)
Date: Thu Jul 16 2009 - 03:22:02 CDT

Dear Nancy,
with the command <<radial rdf 0.5 30 :WAT>> you calculate the rdf for
water itsself. However, I guess you are looking for the distribution of
your water close to the inner walls of your nanotubes.
You can do this like this

radial rdf 0.5 15 :WAT_at_O "mask of your carbon atoms" closest

in that way you define your carbon atoms as solute and the water oxygens
as the surrounding solvent. The 'closest' comand assures, that only the
the distances to the solvent atoms to the closest solute atom are
considered.
However, if you have got water outside your nanotube this will of course
influence the rdf

best regards
Christof

Nancy schrieb:
> Dear amber users and experts,
> I have three kinds of carbon nanotubes which are different in diameter,and they can contain one water chain ,two water chains,four water chains.I calculated radial distribution of water in carbon nanotubes with the command:
> trajin cc_md2.mdcrd
> radial rdf 0.5 30 :WAT
> But results are the same ,only one peak which is out of my expect.I hope that there are one peak, two peaks, four peaks in different diameter's carbon nanotubes. What's more ,i don't understand well what is the differnce of three output rdf files even i have read the manul .Can anybody give me some advice ? Thanks in advance!
> Nancy
>
>
>
>
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>



_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber