[gmx-users] Re: g_rdf calculations for monolayer

[Pim Schravendijk]

> Dear Users
>   I have some problem about g_rdf  calculation for monolayer system.
> My system is porphyrazine monolayer at air-water interface. I tried to calculate the rdf for water around the center of mass of porphyrazine, but the result is still not nomalized. I mean it does not goes to 1 at the long distance. 
> My questions are that
> (1) Can I use g_rdf for calculating such a system
> (2) If I can, how should I do to get normalized rdf?

g_rdf in the CVS version has an -xy option, this might do the trick.
Depending on how your system looks like you might want to also define a 
bottom and top z inbetween which the rdf is made, but you'd have to tweak 
to program a bit to enable this. Actually it shouldn't be a bad idea at 
all to include this there.

(Late reaction, cleaning up my mailbox)

--
Pim Schravendijk - PhD Student
Max Planck Institute for Polymer Research
http://www.mpip-mainz.mpg.de/~schraven/