[gmx-users] Selection of water molecules

[anupama sharma]

Dear users,
I have to calculate the Pair Distribution Function of water present in my
system near protein surface at 5 angstorm region for which I already did
the indexing using gmx select (dynamic indexing). But when I tried to
calculate the Pair Distribution Function using gmx rdf, I am getting option
as to select the reference "the atoms present in one frame", not the
atom/molecule for the system within a defined region and hence, I am unable
to calculate the RDF of water molecule within a defined region for the
whole trajectory which I want to do. Is there any possibility in gromacs to
do so. I'll highly greatful if any one can help.

Thanks in advance
With regards,
Anupama