How to centralize membrane on Z = 0

User discussions
1

GROMACS version: 2022
GROMACS modification: No

Hi,
I’m trying to perform so analysis on a POPG lipid bilayer which requires the bilayer to be centered in the Z = 0 coordinate.

I’ve trying the following comands:

gmx trjconv -f md.xtc  -s md.tpr -pbc whole -o md_0-100ns.xtc -center -n c218.ndx -e 100000

gmx trjconv -f md.xtc  -s md.tpr -pbc mol -o md_0-100ns.xtc -center -n c218.ndx -e 100000

I tried using the whole POPG membrane as the group for centering, as well as the last carbon atom in the lipid tails.

after centering the membrane I also tried running the xtc file through the trjconv comand again using -center 0

gmx trjconv -f md_0-100ns.xtc -s md.tpr -pbc mol -o md_0-100ns.xtc -center 0

But, nothing seems to work, the membrane seems to be centered but not on z = 0.

I’m using a third party tool (LOOS) for the analysis so I can’t really tweek this so the membrane centered in other coordinate works for the analysis.

Thanks

2

A very brutal solution may be that you take the centre of mass of your membrane along z (gmx traj -f memb_trajectory.xtc -s memb_binary.tpr -nox -noy -com -ox com_membrane.xvg) and you use its average to translate the whole bilayer (e.g. gmx trjconv -f memb_trajectory.xtc -s memb_binary.tpr -trans 0 0 -value_of_mem_COM -o trans_memb.xtc). This will make so that the average position of the com of the membrane along z will be positioned in z=0 in the trajectory. If the com’s z doesn’t fluctuate a lot it may be a good approximation of having the membrane centered in z all the time.

4

Thanks for your reply, turns out that the issue with my analysis wasn’t the membrane centering. But thanks.