[gmx-users] how to define an index file

[Mark Abraham]

----- Original Message -----
From: Moeed <lecielll at googlemail.com>
Date: Wednesday, May 19, 2010 4:41
Subject: [gmx-users] how to define an index file
To: gmx-users at gromacs.org

> 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)..

That depends what you want to measure. If you care about the magnitude of the interaction of any particular group of 20 with any other group, then you'll need each in a separate index group to create separate energy groups in your .mdp file.

> 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

You're doing something perverse. Give make_ndx -f your proper 125-hexane .gro file. See make_ndx -h for clues on what file formats are expected for what input parameters.

Mark