Thanks for the quickly answer. I used 3.3.3 and 3.3.1 version and the
lipids of a monocape are above to the other. The lipids are jumping yet
after all those changes. I proved each option separately and some
combinations of them.
trjconv -s a.tpr -f a.xtc -o b.xtc -center
trjconv -s a.tpr -f b.xt
If you use the new version of Gromacs (3.3.3), there are several options that
work nicely. Try each of them separately, probably one of them will work, maybe
a combination will be necessary based on how much your lipids jump around.
trjconv -center
(choose DPPC for centering)
trjconv -pbc res
Hi:
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 he
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