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
criteria.
The output index file contains all the atoms which satisfy the specified
criteria.
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
molecules"
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)?
thanks,
Oleksandr
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