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

Yinghong xieyh at hkusua.hku.hk
Sat Oct 15 01:09:09 CEST 2005

Dear Dr. Tsjerk:

Many many thanks for your detailed explanation. I am trying it later although it is difficult for me. 

As you said, my base was a parallelogram with angles of 120 and 60 degrees. I know, with two more images, a hexagon could be obtained, and with many images, many hexagons will be seen, that is ok?

Breifly, I just want to be made sure about the following two things:

1. In defining the simulation box, could I use this parallelogram as my box instead of a whole hexagon? In other words, one third within a hexagon (monoclinic cell) is enough for my simulation, can I define it as described previously?

2. While using "editconf" to generate the box, the option "-bt tric" is necessary in my case?

Thanks, if not mind, please give me direct answers about the two questions above.

Thanks again.

Xie Yinghong
Hong Kong University

>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
>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,
>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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