[gmx-users] center

Malihe Hasanzadeh ml.hasanzadeh at gmail.com
Sun Dec 6 12:39:59 CET 2015

I have run a ligand-protein MD simulation for 50 ns by gromacs 5.0.5. At
the end of simulations, molecule is out of the box.I have used from two
below command for center but neither of them isn't work and molecule still
is out of box.

trjconv -f md300.trr -o md300t.xtc -fit rot+trans -s md300.tpr
trjconv -f md300.trr -o md300t.xtc -pbc mol -center -s md300.tpr

So how to center the molecule before going for analysis?

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