Hi. After packing lipid and water in PACKMOL, when I run the minimisation step, all the water from the upper leaflet go to below the lower leaflet. Could you help me find the solution of this problem? I am attaching the screenshots of the minimised system.
Hey Manasa,
Unless I am missing something major, the system has no major issues. In the image you have shown the i looks like a the lipids have moved to the top of the periodic boundary. If its bothers you the command gmx trjconv -f [traj/gro filename] -s [tpr filename] -center -pbc mol -ur compact -n [index filename] (make sure to read the docs for gmx trjconv) will allow you to re-image the lipids into the center of the simulation cell.
Best,
Kyle