Make Index of non hydrogen Atom in Gromacs

User discussions
1

GROMACS version: 2024.2.
GROMACS modification: No
Hi, In this command, why should i add * after H?
Is that related to any chemmical concept?

gmx make_ndx -f jz4.gro -o index_jz4.ndx
…

0 & ! a H*
q

2

The syntax of gmx make_ndx should be better documented, indeed. The * does not have anything to do with chemistry, but it is a selection wildcard, meaning that you select all atoms (by name) that begins with H in this case. Then the ! inverts that selection.

So, the final selection will be all atoms in group 0 (System) that does not have atom name beginning with H.

3

tnx 👍🙏