[gmx-users] distribution of water molecules in system

[Turgay Cakmak]

Dear Gromacs Users,

I want to show distribution of water inside the peptide based cylindirical
nanofiber. To do this:

1) I created an index file which contains OW atoms (=Oxygen atoms belongs
to the water molecules)

 2) Then, I used the following command:

g_rdf   -f   traj.xtc   -s OW.ndx   -o rdf.gro

In this step, I should have choosen 2-groups, that is: Select a reference
group and 1 group.

Question 1) I chose OW for both groups.. But, I am not sure whether this
choice is correct or not.. That is, instead, should I have chosen Peptide
for a reference frame and OW for group 1?

Question 2) Can I also use g_rdf command to show distribution of water
inside the peptide based cylindirical nanofiber?

I really appreciate your help.

Turgay