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
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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