[gmx-users] gromacs versus amber boxsize

servaas michielssens servaas.michielssens at student.kuleuven.be
Tue Jan 29 12:57:13 CET 2008

I ran the following command in gromacs:
editconf -bt dodecahedron -f p61_vac_gro.gro -o p61_vac_dod.gro -d 0.8

The equivalent command in amber:
solvateoct p61_vac.pdb TIP3PBOX 8.0

As far as I understand this, both command created a box were the edges are 0.8 nm away from the solute. But the resulting image distance (d in the manual) in gromacs is:
and in amber:

This is makes a hugde difference in the number of water atoms to add.
Does anyone has an explanation for this paradox?

kind regards,

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