[gmx-users] Octahderal box

[Joanne Hanna]

Hello

Right I think I am following, could you please confirm if this is correct:

So the reason the unitcell looks triclinic is because this is what gromacs bases the octahedron on and

the reason the enzyme looks as though it is sticking out of a cube is because when simualting with pbc = xyz  gromacs puts the particles in a brick formation and therfore when i am simulating the protein that looks like its not solvated will be fully solvated by the next brick in the formation?

Sorry if i'm being obtuse.

Thanks for all your help
Jo

Joanne Hanna
Department of Chemistry
University of Warwick
Coventry
CV4 7AL

J.F.Hanna at warwick.ac.uk
>>> spoel at xray.bmc.uu.se 09/10/05 15:07 PM >>>
On Sat, 2005-09-10 at 12:04 +0100, Joanne Hanna wrote:
> Hi
> 
> Thanks, this works. does this mean that i should now use the new *.gro file i have generated as the coordinates for water are quite different.
No it is identical for mdrun, which works with a triclinic
representation of the truncated octahedron. See manual.
> 
> Thanks for your help
> Jo
> 
> Joanne Hanna
> Department of Chemistry
> University of Warwick
> Coventry
> CV4 7AL
> 
> J.F.Hanna at warwick.ac.uk
> >>> spoel at xray.bmc.uu.se 09/10/05 07:46 AM >>>
> On Fri, 2005-09-09 at 21:25 +0100, Joanne Hanna wrote:
> > Hi
> > 
> > I am having some difficulties with a truncated octahedron box.
> > 
> > I have made the box using:
> > 
> > editconf -f ENZ.pdb -d 1.0 -bt octahedron -o box.gro
> > 
> > viewing this in rasmol with the unitcell gives me what looks like a triclinic box.
> > 
> > After solvating this using:
> > 
> > genbox -cp box.gro -cs spc216.gro -o solv.gro
> > 
> > and viewing this in vmd i get what appears to be a cubic box with the enzyme not centered and sticking out of the solvated box.
> > 
> > Does anyone have any ideas where i am going wrong?
> > 
> 
> try
> trjconv -ur compact
> 
> > The output from the editconf is:
> > 
> > Read 5213 atoms
> > Volume: 309.565 nm^3, corresponds to roughly 139300 electrons
> > No velocities found
> >     system size :  6.557  7.485  6.307 (nm)
> >     diameter    :  7.941               (nm)
> >     center      :  3.329 10.051  3.262 (nm)
> >     box vectors :  6.557  7.485  6.307 (nm)
> >     box angles  :  90.00  90.00  90.00 (degrees)
> >     box volume  : 309.56               (nm^3)
> >     shift       :  1.642 -3.022  0.796 (nm)
> > new center      :  4.970  7.029  4.058 (nm)
> > new box vectors :  9.941  9.941  9.941 (nm)
> > new box angles  :  70.53 109.47  70.53 (degrees)
> > new box volume  : 756.24               (nm^3)
> > 
> > gcq#231: "Let's Go Hang Out In a Mall" (LIVE)
> > 
> > and the bottom of the *.gro looks like:
> > 
> >   514PHE    HE1 5206   7.728   5.684   1.408
> >   514PHE    CE2 5207   7.795   5.899   1.651
> >   514PHE    HE2 5208   7.756   5.936   1.735
> >   514PHE     CZ 5209   7.724   5.804   1.578
> >   514PHE     HZ 5210   7.635   5.773   1.609
> >   514PHE      C 5211   8.091   5.970   1.193
> >   514PHE     O1 5212   7.983   5.994   1.114
> >   514PHE     O2 5213   8.194   5.886   1.163
> >    9.94094   9.37241   8.11675   0.00000   0.00000   3.31365   0.00000  -3.31365   4.68621
> > 
> > Any advice would be greatly appreciated.
> > 
> > Thanks
> > 
> > Jo
> > 
> > 
> > 
> > Joanne Hanna
> > Department of Chemistry
> > University of Warwick
> > Coventry
> > CV4 7AL
> > 
> > J.F.Hanna at warwick.ac.uk
> > _______________________________________________
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> > gmx-users at gromacs.org
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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