[gmx-users] centering a protofibril in a box

Adriana Garro adrianagarrosl at gmail.com
Thu Nov 6 12:13:40 CET 2014

Dear all,

I am trying to center a protofibril in a box, but respect to its first
monomer. (the result would be the protofibril shiftted to the botton of the
I used
trjconv -f protofibril.pdb -n index.ndx -center -s  protofibril.pdb -o

I did an index for the residues corresponding to the first monomer and that
is which I chose as "select group for centering" but when I visualize the
System with vmd the protofibril appears in the center of the box but as it
was just one molecule.
Thanks in advance!


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