[gmx-users] Make an index file

Shima Arasteh shima_arasteh2001 at yahoo.com
Sat Apr 28 19:57:21 CEST 2012

Dear gmx users,
I want to simulate POPC in water. In equilibration step, I have to make an index file. But when I enter this command, I do not know to choose which group to make a suitable .ndx file which matches the molecule types and molecules sections in .top file .

The .top file contains these:

[ moleculetype ]
; Name   nrexcl
POPC      3

[ system ]
; name
POPC in water

[ molecules ]
; name    number
POPC     128   
SOL      3800


It is the command I enter:

# make_ndx -f em.gro -o index.ndx
  0 System              : 18056 atoms
  1 Other               :  6656 atoms
  2 POP                 :  6656 atoms
  3 Water               : 11400 atoms
  4 SOL                 : 11400 atoms
  5 non-Water           :  6656 atoms

 nr : group       !   'name' nr name   'splitch' nr    Enter: list groups
 'a': atom        &   'del' nr         'splitres' nr   'l': list residues
 't': atom type   |   'keep' nr        'splitat' nr    'h': help
 'r': residue         'res' nr         'chain' char
 "name": group        'case': case sensitive           'q': save and quit
 'ri': residue index  

Now, what is the correct answer? Anybody can suggest me? 

Thanks in advance,

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