[gmx-users] How to choose two atoms at the same time, using g_select selection.dat

Justin A. Lemkul jalemkul at vt.edu
Thu Apr 26 03:24:21 CEST 2012

On 4/25/12 9:19 PM, mu xiaojia wrote:
> Dear gmx users,
> I may have a silly question, how to make a group of two atoms from the same
> molecule?
> e.g, I want to make an "HN" group of both H and N from my 2nd residue,
> I know for single one, commands in *.dat file is like:
> nameN = resnr 2 and name N;
> nameH = resnr 2 and name H;
> nameN;
> nameH;
> I guess "merge" or "plus" might be helpful,I think it should be done something
> like: "nameN_H = resnr 2 and name N ?? resnr 2 and name H", so it is an
> intramolecular combination between N and H; it shouldn't be done afterwards,
> otherwise it would be an intermolecular combination.
> Thanks very much! g_select is really powerful, and hopefully there would be more
> examples.

g_select is more suited for complex groups that are dynamic or otherwise based 
on geometric criteria.  If you're trying to make a simple group that consists of 
2 atoms, make_ndx is easier, and using a plain text editor will be easiest, i.e.:

[ my_group ]
  1  2



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


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