[gmx-users] pbc problem

[shahab shariati]

Dear jkrieger

I used 2 times trjconv tool:

1) trjconv -f npt.xtc -s npt.tpr -n index.ndx -o 2npt.xtc -pbc nojump

2) trjconv -f 2npt.xtc -s npt.tpr -n index.ndx -o 3npt.xtc -pbc mol -center


Dear Mark

I selected all lipid atoms for centering.

With my manner, pbc problem was solved just for lipids and not for drug
molecule which is put inside water molecules in top leaflet. This pbc
problem cause to drug molecule be in top and bottom leaflets, while I want
to study translocation of the drug molecule from water to lipid bilayer.
I want to solve this problem for drug molecule.

If my manner is wrong, please tell me true way.

Best wishes.