servaas michielssens wrote:
I made a mistake in the numbers, but the question remains:
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:
121.3092
and in amber:
110.5103716
What shapes were these commands creating? How are you measuring this
image distance?
Mark
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