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

Justin Lemkul jalemkul at vt.edu
Wed Apr 3 23:54:50 CEST 2013

On 4/3/13 11:13 AM, Oleksandr Sushko wrote:
> 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)?

It would help to know exactly what your selection syntax was.  I think you can 
use something like "same residue as (within ...)" for your selection, but I 
haven't tried it.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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