[gmx-users] How to use make_ndx in script to combine 2 groups

Agnivo Gosai agnivogromacs14 at gmail.com
Wed Nov 19 23:47:55 CET 2014

Hello Users

I plan to use make_ndx in a script for passing it on to grompp by combining
two groups of molecules in my system.

When running interactively I use make_ndx  -f xyz.gro -o index.ndx
Choose groups :

group1 | group 4

hit enter

type q

hit enter

I was thinking of putting these set of interactions on a script. Can I type
group1 , group4 , | , q on a .txt file and pass it onto make_ndx in the
script. I have not seen myself , but I am speculating. Please bear with my

Thanks & Regards
Agnivo Gosai
Grad Student, Iowa State University.

More information about the gromacs.org_gmx-users mailing list