Changing the group name in gmx make_ndx

User discussions
1

GROMACS version: 2025.3
GROMACS modification: No

Is there a possibility to change the name of a certain group using its original number and not its number? To the best of my knowledge, the following make_ndx options do not offer such functionality:

nr : group ‘!’: not ‘name’ nr name ‘splitch’ nr Enter: list groups
‘a’: atom ‘&’: and ‘del’ nr ‘splitres’ nr ‘l’: list residues
‘t’: atom type ‘|’: or ‘keep’ nr ‘splitat’ nr ‘h’: help
‘r’: residue ‘res’ nr ‘chain’ char
“name”: group ‘case’: case sensitive ‘q’: save and quit
‘ri’: residue index

For instance,
name 3 LIG
works correctly but
name “NPX” LIG
or
name NPX LIG
has no action on group names.

2

No, AFAIK that’s not possible. Some quality-of-life improvements of gmx index that include easier naming of groups are currently in the works, but it’ll take until 2027 for those to make it in. For now, you’ll have to just list the groups by pressing enter and using the group number, which is not that much more of a hassle IMO.