[gmx-users] fixing PBC view

[Netaly Khazanov]

Hi All,
My system is including the small compound with penetrates the membrane
lipids. I've ran the MD simulation and now trying to get rid off the PBC
view and create a nice movie. The problem that I've managed to fix PBC view
of the lipids, however the location of small compound still indicates the
wrong position related to membrane. Any ideas how to fix it will be
appreciated.
The command that I used:
 trjconv_d -s md.tpr -f md.xtc -o md_noPBC.pdb -pbc mol -center -n -ur
compact # centering on POPC group
I've used the numerous variation  but none does work.

Thanks in advance

-- 
Netaly