[gmx-users] trjconv pbc membrane

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

Re: [gmx-users] trjconv pbc membrane

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

Re: [gmx-users] trjconv pbc membrane

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