[gmx-users] pbc problem

shahab shariati shahab.shariati at gmail.com
Thu Oct 24 08:09:18 CEST 2013

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.

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