[gmx-users] Re:Which kind of box?

[Tsjerk Wassenaar]

Hi Xie Yinghong,

Since one of your vectors is exactly perpendicular to the other two, lets
just focus on the base. And remember that what goes in 2D counts in 3D too.
Your base is a parallelogram with angles of 120 and 60 degrees. Now copy
that several times. Then take one of the corner points in the centre. Draw
lines to mark the borders where any point in the plane lies closer to that
point than to any of the other corner points. You will get a marked shape,
which is generally called the Voronoi region. In your case, you'll find that
the Voronoi region of your system is a perfect hexagon. With your third
vector, you'll have a perfectly regular hexagonal prism.

Now if you do it for the other points two, you'll find that the same hexagon
will be located at each corner point in the grid created by the copied
parallelograms. Thus, you can equally well look at your system as an
infinite replicated system of hexagons. These will be connected by the edges
of the original unit cells. Imagine the first vector aligned with the
x-axis, and the central corner point at the origin (thus with one hexagon
centred at the origin) and you'll have one neighbouring hexagon at +1x. Now
you defined your second vector to have an angle of 120 degrees. So in your
case you'll take the second hexagon at -0.5x, +0.866y. But if you look at
the copied system, you'll find that there's also a hexagon at +0.5x,
+0.866y. That's equally valid to take as a second copy, and if you draw a
line connecting from the origin to that, it will have an angle of 60 degrees
with the positive x-axis. In other words, with an angle of 60 degrees (and
equal vector lengths) you have defined the exact same infinite simulation
system.

I encourage you to draw the things I explained above. Also google for
'lattice', 'voronoi', 'triclinic' and do have a look at the paper of Bekker
I suggested before.

I hope this helps,

Tsjerk

On 10/14/05, Yinghong <xieyh at hkusua.hku.hk> wrote:
>
> Dear Tsjerk:
>
>  Thanks for your kind help. And, I need furthur confirmation about the
> following things.
>
>  My box is actually based on hexagonal prism, but its cross-section is not
> a hexagon. In fact, it is only a monoclinic cell totoally with 6 faces in
> the whole box, instead of 8 faces in hexagonal prism. Accordingly, is my
> previous definition correct?
>
> So, in such case, I used "editconf -bt tric" to build the box, is that
> ok????? As told by you, all the box types are the same for simulation, to
> this point, I need your confirmation, thanks.
>
> By the way, what is the meaning of the third angle equal to 60 degree? I
> searched many previous achieves, 120 degree was always adopted.
>
>  Xie Yinghong
>
> HongKong University
>
>    >Hi Yinghong,
>
> > I believe you want to set up a hexagonal prism according to your
> previous
> > mails, and the procedure you outline would be consistent with that. For
> >visualizing the system represented by a triclinic box the command for
> >trjconv is also correct. You might also want to try compact and rect for
> -ur
> >and compare the results, keeping in mind that it's all the same system,
> but
> >just different representations (interconversion of box types).
>
> >Do make sure that the box dimensions are large enough to contain your
> >protein when setting up the box with editconf. By the way, coming to
> think
> >of it, you may as well set the third angle to 60 degrees. That will give
> the
> >same box :p (that will describe the same lattice), but is more likely to
> >comply to Gromacs prerequisites for boxes.
>
> >Cheers,
>
> >Tsjerk
>
>
> On 10/13/05, Rodrigo Reston <rodrigoreston at yahoo.com.br> wrote:
> >
> > I'm not sure if your problem is this one... Have you
> > visualized what the triclinic shape looks like? If you
> > haven't, search for the word "triclinic" on Google
> > Images to see one and maybe then it'll help you design
> > the best approach to encase your system (by the way,
> > do that to the other shapes available in editconf).
> > Also, you might not need to specify the dimensions of
> > the triclinic box - perhaps, just using the option -d
> > and typing the distance (like [0.5] nm) from your
> > molecule to anyone of the triclinic box faces will do.
> > Rodrigo S. Reston, BSc.
> > UFMG, Brazil.
> >
> > --- Yinghong <xieyh at hkusua.hku.hk> wrote:
> >
> > > Dear users:
> > >
> > > I am very strange with the concept of triclinic, so
> > > I need your instruction for the choice of my
> > > simulation box.
> > >
> > > In my current system, the lengths of a b c are
> > > respectively 5.0, 5.0, 10.0nm, and the angles
> > > between bc, ac, ab are 90, 90 and 120 degrees.
> > > Because of my misunderstanding of triclinic, maybe,
> > > the following steps are somewhat wrong, can you help
> > > me to point them out?
> > >
> > > 1. editconf -f mole.gro -o out.gro -bt tric -box 5
> > > 5 10 -angles 90 90 120 -c
> > > Should I use the option "-bt tric" here? If not
> > > triclinic, possibly, "-bt tric" is wrong.
> > >
> > > 2. genbox -cp out -cs -p topol.top -o b4em.gro
> > >
> > > 3. grompp -v -f em -c b4em -p topol -o box.tpr
> > >
> > > 4.trjconv -f b4em.gro -s box.tpr -o b4em2.gro -ur
> > > tric -pbc inbox ---- for visualization only.
> > > What should my choice for options "-ur & -pbc" in
> > > this case?
> > >
> > > Urgent equiry and any help will be greatly
> > > apprieciated.
> > >
> > >
> > > Xie Yinghong
> > > Hong Kong University
>
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--

Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336
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