[gmx-users] how to define an index file

Moeed lecielll at googlemail.com
Tue May 18 20:39:58 CEST 2010


Hello,

I am trying to create an index file to get interaction energies between
hexane (C6H14, 20atoms) molecules. I have 125 hexane molecules in my system.
To do this how should I define my index groups. Should I include all 125
molecuels in index file? now I have only the first 20 atoms (first
molecule)..




make_ndx -f Hexane-0.25nm3-index.gro -o index.ndx

Reading structure file

-------------------------------------------------------
Program make_ndx, VERSION 4.0.7
Source code file: gmx_fatal.c, line: 511

Fatal error:
Unexpected end of file in file Hexane-0.25nm3-index.gro at line 2
(Source file confio.c, line 725)

Hexane-0.25nm3-index.gro:

[ Hexane ]
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20


Thanks,
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