GROMACS version:2025.4
GROMACS modification: No
Dear GROMACS users,
I am working with ionisable lipid–membrane lipid bilayer system simulated for 500 ns. I would like to apply PBC corrections to obtain a proper trajectory for analysis.
I have used the following commands:
gmx trjconv -s npt.tpr -f npt.xtc -o whole.xtc -pbc whole
gmx trjconv -f whole.xtc -s npt.tpr -pbc nojump -o nojump.xtc
gmx trjconv -f nojump.xtc -s npt.tpr -n index.ndx -pbc mol -center -o centered.xtc
The water and bilayer remained consistent with these commands. However, I still observe that the ionisable lipid jumping between the upper and lower water layers due to pbc before penetrating into the lower leaflet.
Could anyone kindly suggest the correct procedure for handling these PBC corrections to analyse the vertical distance of the center of mass of the ionizable lipid to the bilayer center without any jumps?
Thank you.