[gmx-users] gromacs versus amber boxsize -correction-

Mark Abraham Mark.Abraham at anu.edu.au
Tue Jan 29 13:37:58 CET 2008

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?


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