Re: [gmx-users] Can't center box with trjconv

Try e.g. trjconv -pbc mol -trans ? ? ? to have your molecule not span the edges first. You might also need a trjconv -pbc nojump and trjconv -pbc -mol again afterwards before centering. 25 okt 2012 kl. 13.44 skrev Ignacio Fernández Galván: > I must be doing something wrong, but I can't get trj

[gmx-users] Can't center box with trjconv

I must be doing something wrong, but I can't get trjconv to center the simulation on a residue. The simulation box is cubic, the system is formed by an 8-atom frozen molecule and 800 water molecules. I try to center the box with: $ trjconv -f system.cpt -s system.tpr -o conf.gro -center (sys