Gmx ndx usage

User discussions
1

Continuing the discussion from Removing pbc effect:

I am also simulating a protein with multiple chains, and am unfamiliar with how to find the atom numbers of each chain so that I can try making an ndx file to remove pbc. Any advice would be greatly appreciated, thank you.

2

Hi L_k,

using Selection syntax and usage — GROMACS 2020.5 documentation in combination with gmx select can help you here.

3

Hi cblau,

Thank you for the suggestion! I will give it a try.