t.a.wassenaar at chem.rug.nl
Thu Feb 19 15:06:01 CET 2004
If you use -center 0 0 0 it will be centered around the origin, so it
will be positioned at the corner of the box. However, since you pbc it
shouldn't matter at all. It is mainly for visualization that you would
want to center, and it may decrease jumping across box borders during
simulation. If you really want to have it centered:
editconf -f input.pdb -d 0.8
editconf -f out.gro -o centered.pdb -center box[x]/2 box[y]/2 box[z]/2
box[x], box[y] and box[z] are the first three numbers at the end of out.gro
Kay Gottschalk wrote:
> I don't know if I am doing it correctly: I centered my molecule wit
> editconf -f input.pdb -center 0 0 0 -o centered.pdb, then tried to
> build the box around it with editconf -f centered.pdb -d 0.8 -center 0
> 0 0. Still it doesn't seem to be centered. It is important that it's
> centered? Since we pbc, it should make no difference, I think...
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