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.
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