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

Yinghong xieyh at hkusua.hku.hk
Fri Oct 14 20:06:41 CEST 2005

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.

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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