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