How to select lipids close to molecule during simulation

User discussions
1

GROMACS version:2019-4
GROMACS modification: No

We want to analyze how lipids are ordered close to moving molecule in membrane during simulation.
How can we select lipids around 1 nm from a molecule from whole trajectory ? We would like to examine order parameters in various frames. We tried with a command "gmx select -select 'resname “LIPID” and within 1 of resname “LIG” ’ but it was not succesfull.

BR,
Maija

2

Hi,
Maybe you already have look at it, but maybe this page can help you
https://manual.gromacs.org/current/onlinehelp/selections.html?highlight=selection

Regards
Alessandra

3

Thank you! We have tried to select based on these ones, but somehow lipids are not selected as molecules just only part of chain. We think that the calculated order parameter with these parts of lipids does not sound reasonable.

BR,
Maija

4

Take a look at Membplugin for VMD
https://sourceforge.net/p/membplugin/wiki/ScdOrderParameter/
also
https://pubs.acs.org/doi/10.1021/acs.jctc.7b00643

Hope these help
Paul