On Tue, 29 Jan 2008 13:14:21 +0100
"servaas michielssens" <[EMAIL PROTECTED]> 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
is there any reorientation in volved?
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)
amber or gromacs manual?
in gromacs is:
121.3092
and in amber:
110.5103716
Are the d the same in both programs?
The definitions of dodecahedron are different in gromacs and gromos.
could be a similar problem in with amber!
Note however that the gromacs definition decreased the volume as
compared to gromos.
This is makes a hugde difference in the number of water atoms to add.
Does anyone has an explanation for this paradox?
kind regards,
servaas
-----------------------------------------------------
XAvier Periole - PhD
NMR & Molecular Dynamics Group
University of Groningen
The Netherlands
http://md.chem.rug.nl/~periole
-----------------------------------------------------
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