IGDIST is for solvent-solvent g(r); you only need one selection:
coor anal water select type OH2 end -
firstu 21 nunit 1 skip 10 - ! trajectory specification
igdist 31 ioh 32 ihh 33 - ! flag to do the solvent-solvent g(r)
mgn 100 dr 0.1 - ! comp. g(r) at MGN points separated by DR
rsph 999.9 - ! use ALL waters for rdf calculation
xbox @6 ybox @7 zbox @8 ! and we did use PBC
ISDIST is as you say for g(r) of solute (site(s)) vs solvent, and is what you should use:
! g(r) backbone amide hydrogen - water oxygens
! if a single solute atom is looked at the MULTi keyword is not necessary
! when several solute atoms are specified as the site, their average position
! will be used as the reference position if MULTi is not present
open unit 21 read unform name @9pept500.cor
open unit 31 write form name @9pept500.gonh
coor anal select type oh2 end - ! Water oxygens
site select type H end multi - ! and the amide hydrogens
firstu 21 nunit 1 skip 10 - ! trajectory specification
isdist 31 - ! do the g(r) (here solute-solvent)
mgn 100 dr 0.1 - ! comp. g(r) at MGN points separated by DR
rsph 999.9 - ! we use ALL waters for the calculation
xbox @6 ybox @7 zbox @8 ! and we did use PBC
The complication in your case is that COOR ANAL does not allow you to specify that the center of mass of each urea molecule should be used. A work-around is to pick an atom close to the center of mass: sele resn urea .and. type C2 end
