[gmx-users] solvent atom numbers

[Giorgos Karvounis]

Dear all,

i have this little problem with solvent atom numbers. I want to do some
analysis of water molecules (e.g. the lifetime of specific water
molecule(s) close to hydrogen bond )  and so i want to find out which of
the water molecules of the box stay within a certain distance from the
c.o.m of my peptide. Using trjorder, i create a xtc file but with the
rearanged molecules, i can find how many of the water molecules are
within that distance but this doesnt tell me which of the water
molecules of the original run belong to that distance. g_mindist tells
me the number of contacts (and min_distance) but not the atom-number.
So, at the end i am not sure of which atoms (water molecules) to
analyse.I hope this makes sense.

Thanks

Giorgos