PBC correction for drug–lipid bilayer system (GROMACS 2024.5)

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Dear GROMACS users,

I am working with a drug–membrane lipid bilayer system simulated for 500 ns using GROMACS 2024.5 (no modifications). I would like to apply PBC corrections to obtain a proper trajectory for analysis.

I first made broken molecules whole:
gmx trjconv -s prod.tpr -f prod.xtc -o pbc_whole.xtc -pbc whole

Then I centered the system around an atom close to the center of mass:
gmx trjconv -s prod.tpr -f pbc_whole.xtc -o pbc_center1.xtc -center -n center.ndx

However, I still observe that the drug molecule occasionally jumps between the upper and lower leaflets, even though the water and bilayer remain consistent with the first frame.

I also tried the following options, but the issue persists:

  • gmx trjconv with -pbc nojump

  • gmx trjconv with -pbc mol

Could you kindly suggest the correct procedure for handling PBC corrections in such drug–bilayer systems?

Thank you for your guidance.

Mohan