[gmx-users] g_dipoles: "index group is not a set of the whole molecules"

Oleksandr Sushko o.sushko at eecs.qmul.ac.uk
Wed Apr 3 17:13:44 CEST 2013

Dear Gromacs users,
can you help me please with next issue:
I'm analysing solvation shell of water molecules around a protein.
I use g_select to select different layers of water based on distance 
The output index file contains all the atoms which satisfy the specified 
For some molecules on the edge only some atoms are within the specified 
distance from protein.
So some molecules in the selection are represented only by 1 or 2 atoms 
out of 3.

Such selection works fine for example for g_hbond, but it does not work 
for g_dipoles.
The error in case of g_dipoles is: "index group is not a set of whole 

is there a smart way (except manual editing of .ndx file) to select the 
whole molecules within some distance from protein (with COM within 
specified distance from protein surface)?


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