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

Florian Haberl Florian.Haberl at chemie.uni-erlangen.de
Tue Jan 29 13:43:13 CET 2008


On Tuesday, 29. January 2008 13:14, 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

With -d and a triclinic box the size of the system in the x, y and z
directions is used. With -d and cubic, dodecahedron or octahedron boxes, the
dimensions are set to the diameter of the system (largest distance between
atoms) plus twice the specified distance. [from editconf -h]

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

generates a truncated octahedron periodic box

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

so you generate two different boxsizes or types.

> kind regards,
> servaas



 Florian Haberl                        
 Universitaet Erlangen/ Nuernberg
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 Telephone:  	+49(0) − 9131 − 85 26573
 Mailto: florian.haberl AT chemie.uni-erlangen.de

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