[gmx-users] selecting atoms in index file

Hermann, Johannes J.Hermann at lrz.tu-muenchen.de
Thu Sep 7 11:16:15 CEST 2017

Dear Golnaz,

do you know the number (index) of the respective atoms? E.g. open the 
.gro file in vmd and look for the atoms?

If there are not too many atoms, you can manually edit your index file. 
E.g. create a default index file (gmx make_ndx) and add the subset of 
indexes with a new selection definition:


[ MySelection]

23 57 75


All the best


On 07.09.2017 11:02, G R wrote:
> Dear All,
> I want to create an index file and select some especial atoms in a surface.
> My problem is that I have only one residue for the whole surface. How can I
> select the atoms on the surface as a different groups in my index file?
> Thank you in advance,
> Golnaz

*Technische Universität München*
*Johannes Hermann, M.Sc.*
Lehrstuhl für Bioverfahrenstechnik
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Email: j.hermann at lrz.tum.de

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