[gmx-users] trjconv pbc membrane

maite lopez cabezas lopezmai at gmail.com
Wed Jul 16 22:10:56 CEST 2008

I equilibrated a DPPC  membrane that I built. I want to take a
snapshot for doing some protein-membrane simulations, but first i have
to do somethings for eliminating the lipids out of the box. I have
tried with pbc and fit options like people say in the list and it
doesn't work. Anybody can help me, please?

I did things like that and more too (with many combinations):

trjconv -s a.tpr -f a.xtc -o b.xtc -center tric -ur compact -pbc none
trjconv -s a.tpr -f b.xtc -o c.xtc -fit rot+trans

trjconv -s a.tpr -f a.xtc -o b.xtc -center tric -ur compact -pbc nojump
trjconv -s a.tpr -f b.xtc -o c.xtc -pbc whole
trjconv -s a.tpr -f c.xtc -o d.xtc -fit rot+trans

I'll apreciate any help,

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