[gmx-users] Octahderal box
Joanne Hanna
J.F.Hanna at warwick.ac.uk
Sat Sep 10 20:27:43 CEST 2005
Sorry, right I am following now. So the -pi option of g_minidist might be useful for that.
Thanks for the advice.
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 19:05 PM >>>
On Sat, 2005-09-10 at 18:49 +0100, Joanne Hanna wrote:
> Hello again
>
> Sorry i am a bit confused, again. When you say you have to verify if the box is big enough what exactly do you
> mean? isn't using -d 1.0 (my vdw is 1.0) at the editconf stage enough to ensure that the box is large enough, and that no part of my protein is closer than 1.0 to the edge of the box? or does that mean that if the protein appears to be sticking out of the box that the box is not large enough? Also if there is a tool for verifying the box size could you please tell me which one, it really would be very useful.
You have to check after a simulation, since the protein may unfold or
loops may move away. -d 1.0 does produce a layer of 1 nm, whether that
is enough is for you to decide, although it is comparable to what most
people use.
>
> Many thanks
> 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 18:29 PM >>>
> On Sat, 2005-09-10 at 15:57 +0100, Joanne Hanna wrote:
> > 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?
> Yes. Still you have to verify that your box is large enough, there is
> even a tool for this but I forgot which one.
>
> All crystallographic unit cells can be represented as a triclinic cell.
> >
> > 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
> > > > _______________________________________________
> > > > gmx-users mailing list
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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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--
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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