[gmx-users] index groups

[Justin A. Lemkul]

Moeed wrote:
> *I read thorough the manual on index groups and creating index file. 
> This is the command I tried:
> 
> make_ndx -f index.gro -o index.ndx
> *
> with index.gro you proposed:

I posted an index file suitable for use as is.  It is not a .gro file.  I 
created the index file using a simple text editor.  For a very simple 4-atom 
system, it is probably faster to skip make_ndx.

> 
> [ special ]
>   1  3
> [ all ]
>   1  2  3  4
> 
> error I get:
> 
> Reading structure file
> 
> -------------------------------------------------------
> Program make_ndx, VERSION 4.0.7
> Source code file: confio.c, line: 728
> 
> Fatal error:
> Invalid line in index.gro for atom 1:
> [ all ]
> -------------------------------------------------------
> 
> I thought maybe the group name should be changed... but it is 
> complaining of sth I cant figure out.
> 
> Also I am asking the following Q just for the sake of learning. I dont 
> want to do something blindly :)
> - can you please let me know what is the justification behind using 1 3 
> in first group.  *

These two atoms form a straight line.  By telling editconf to align these atoms 
with the x-axis, it actually does.  Telling edticonf to align the whole molecule 
with the x-axis does not achieve what you want.  For larger structures (like 
proteins) a principal axis is more easily utilized without a special indx group.

> *- I read about default groups. like "system" where all atoms are 
> defined. So why do we need to define "all" group again? *
> 

Because I created my own index.ndx file without using make_ndx.

-Justin

> Thanks,
> *
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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