[gmx-users] editconf

[Tsjerk Wassenaar]

Hi Kay,

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

Cheers,

Tsjerk

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...
> Thanks,
> Kay.
>
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