[gmx-users] making index file

Justin A. Lemkul jalemkul at vt.edu
Wed Aug 25 22:32:52 CEST 2010

jojo J wrote:
> Hello,
> I am trying to make two different groups from residues below. one under 
> the name Solute (residues a and b) and the other for solvent (residue c, 
> SOL).  The only way I know now is to do this by splitting the list of 
> atom numbers [system] (default index file), from 1 to 362 and creating a 
> new directive [SOL] and putting the rest of the atoms under this 
> directory. Can you please help how to do this using the commands like 
> nr, name... I could not do that by reading the help option Thanks

Each [moleculetype] should be its own default group, i.e.:


Making selections from these is trivial.  Unless you've got some bizarre 
topology organization such that you only have a [System] group, then it should 
be very easy to merge groups as necessary.  For instance, if A and B are 
different moleculetypes, merging them can be done with:

A | B

If you need to merge based on subsets of groups and you know the residue 
numbers, you can apply the same concept:

r 1 | r 2

Solvent (SOL) should already be a default group, so I'm not seeing why you have 
to create it yourself.


>  0 System              : 20343 atoms
>   1 a                :    10 atoms
>   2 b                 :   333 atoms
>   3 c                 :  20000 atoms


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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