[gmx-users] distribution of water molecules

[Turgay Cakmak]

Dear all,

I have a box of water molecules and a peptite amphiphile based cylindirical
nanofiber. I would like to find the density distribution of water. To do
this:

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

 2) Then, I used the following command:

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


To be able to continue one needs to choose a reference group and the other
group. How does this work: for example how should I choose these groups?


Also, Could the same procedures be used to compute the distribution of
sodium ions?

Thank you for your help.


Turgay