[gmx-users] get_index

Stéphane Téletchéa steletch at jouy.inra.fr
Thu Jul 5 16:33:08 CEST 2007

Pedro Alexandre de Araújo Gomes Lapido Loureiro a écrit :
>     echo 3 4 5 6 7 | program
> I said many index groups.

Even with hundreds of groups, this is quite trivial, you could use 
something like :

make_ndx -f ini/${molecule}.gro \
          -o ini/${molecule}.ndx &> ini/make_ndx.log <<EOF
1 | 12
13 | 14

This is what i use for instance for coupling solvent and ions (13|14) 
and protein + ligand (1|12).

You can extend your groups as you need (you just need to check first how 
these groups are defined, but this is quite straigtforward and within 
half and hour (using the trials and check method) you'll get the 
complete group list you need (if this is quite logical, you can even do 
it inside a loop). Probably much faster than using a C programming.

scripting + using the regular program is in my humble opinion a far more 
robut approach than modifying the code for your own (think about 
maintenance ...).

Hope this helps,


Stéphane Téletchéa, PhD.                  http://www.steletch.org
Unité Mathématique Informatique et Génome http://migale.jouy.inra.fr/mig
INRA, Domaine de Vilvert                  Tél : (33) 134 652 891
78352 Jouy-en-Josas cedex, France         Fax : (33) 134 652 901

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