[gmx-users] Which kind of box?

[Tsjerk Wassenaar]

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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