Special index group of only a chunk of a bilayer

User discussions
1

GROMACS version: 2020.3
GROMACS modification: No

Hi,

I’m trying to pull a particle into a DOPC bilayer, but I only want the distance to be calculated based only on a portion of the leaflet where the particle is entering through. How do I locate the specific bilayer atoms of the section I need to create a special index group?

Thank you very much!

2

Hi,

How do I locate the specific bilayer atoms of the section I need to create a special index group?Blockquote

to create an index file based on a position you can try the tool gmx select
For selection syntax see https://manual.gromacs.org/current/onlinehelp/selections.html?highlight=selection

Best regards
Alessandra