[gmx-users] Re: g_dipoles: "index group is not a set of the whole molecules"
o.sushko at eecs.qmul.ac.uk
Thu Apr 4 16:12:07 CEST 2013
Justin Lemkul wrote
> 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
>> 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
>> 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
>> molecules within some distance from protein (with COM within specified
>> from protein surface)?
> It would help to know exactly what your selection syntax was. I think you
> use something like "same residue as (within ...)" for your selection, but
> 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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Thanks a lot,
now I used: 'group "SOL" and same residue as within ... of group "Protein"'
and it selected the whole water molecules as I wanted.
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