[gmx-users] making index file

Moeed lecielll at googlemail.com
Thu Aug 26 18:21:06 CEST 2010

Hello Justin,

Please let me explain my naive procedure to make index file so that you can
make comment. I have created the top file for a single solvent molecule.
Then removed [system] , [molecule] directives as well as "#ffgmx.itp". The
[molecule type] is named 'solvent''. I got a sample itp file from a tutorial
and then copied the contents of this modified top file into the file with
itp extention and named it solvent.itp. Then I # included this itp file in
solute. top file and based on  solvated gro file added "solvent 1000" in
[molecule] directive of solute.top. solvated gro contains residues a,b,c for
solute and 'SOL' for the solvent. then I issue the command : make_ndx -f
solvated.gro -o solvated.ndx which lists the residues :

0 System              : 30350 atoms
  1 a                :    10 atoms
  2 b                 :   330 atoms
  3 c              :     10 atoms
  4 SOL                 : 30000 atoms

I am not getting my default groups according to [moleculetype]. Am I missing
sth?  That I am only getting system index group is becase I am only using
user defined residues?

> r1|r2|r3

Merged two groups with OR:
Merged two groups with OR:

  5 r_1_r_2_r_3         :

is giving me
different directives for system, a, b, c, and SOL and one for
 r_1_r_2_r_3 in solvated.ndx. I dont see what the last one is for?!

Residues a, b and c belong to solute and should form one group since I want
to get interaction energy between solute and solvent. How can I create these
two groups (to be included in mdp file energy groups ). I searched the
manual and archive list but never found such details of creating index
files. It seems it is something that everyone knows! :) Please help me..
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