mvogt at es.chem.umass.edu
Mon Nov 29 22:37:48 CET 2004
I've read the archives and I've been trying to center a solute
in a box with solvent and I still can't do it. I have a pdb file
from a trajectory that looks something like this:
w is water and p is protein
The box is 50 Angstroms x 50 Angstroms x 50 Angstroms.
editconf -f start.pdb -o centered.pdb -center 2.5 2.5 2.5
editconf -f start.pdb -o centered.pdb -c
and different versions of gromacs but the resulting centered.pdb always
looks like the starting one. Seems like it should be easy and I'm sure
it's something stupid, but I can't get it.
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