Hi Xie Yinghong,<br>
<br>
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.<br>
<br>
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.<br>
<br>
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.<br>
<br>
I hope this helps,<br>
<br>
Tsjerk<br><br><div><span class="gmail_quote">On 10/14/05, <b class="gmail_sendername">Yinghong</b> <<a href="mailto:xieyh@hkusua.hku.hk">xieyh@hkusua.hku.hk</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<p>Dear Tsjerk:</p>
<p> </p>
<p>Thanks for your kind help. And, I need furthur confirmation about the
following things.</p>
<p> </p>
<p>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?</p>
<p>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.</p>
<p>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.</p>
<p> </p>
<p>Xie Yinghong</p>
<p>HongKong University</p><div><span class="e" id="q_106ece24c62cfd7b_1">
<p> </p>
<p> </p>
<p> </p>
<p>>Hi Yinghong,</p>
<p>> I believe you want to set up a hexagonal prism according to your
previous<br>> mails, and the procedure you outline would be consistent with
that. For<br>>visualizing the system represented by a triclinic box the
command for<br>>trjconv is also correct. You might also want to try compact
and rect for -ur<br>>and compare the results, keeping in mind that it's all
the same system, but<br>>just different representations (interconversion of
box types).</p>
<p>>Do make sure that the box dimensions are large enough to contain
your<br>>protein when setting up the box with editconf. By the way, coming to
think<br>>of it, you may as well set the third angle to 60 degrees. That will
give the<br>>same box :p (that will describe the same lattice), but is more
likely to<br>>comply to Gromacs prerequisites for boxes.</p>
<p>>Cheers,</p>
<p>>Tsjerk</p>
<p><br>On 10/13/05, Rodrigo Reston <<a href="mailto:rodrigoreston@yahoo.com.br" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">rodrigoreston@yahoo.com.br</a>>
wrote:<br>><br>> I'm not sure if your problem is this one... Have
you<br>> visualized what the triclinic shape looks like? If you<br>>
haven't, search for the word "triclinic" on Google<br>> Images to see one and
maybe then it'll help you design<br>> the best approach to encase your system
(by the way,<br>> do that to the other shapes available in editconf).<br>>
Also, you might not need to specify the dimensions of<br>> the triclinic box
- perhaps, just using the option -d<br>> and typing the distance (like [0.5]
nm) from your<br>> molecule to anyone of the triclinic box faces will
do.<br>> Rodrigo S. Reston, BSc.<br>> UFMG, Brazil.<br>><br>> ---
Yinghong <<a href="mailto:xieyh@hkusua.hku.hk" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">xieyh@hkusua.hku.hk</a>>
wrote:<br>><br>> > Dear users:<br>> ><br>> > I am very
strange with the concept of triclinic, so<br>> > I need your instruction
for the choice of my<br>> > simulation box.<br>> ><br>> > In
my current system, the lengths of a b c are<br>> > respectively 5.0, 5.0,
10.0nm, and the angles<br>> > between bc, ac, ab are 90, 90 and 120
degrees.<br>> > Because of my misunderstanding of triclinic,
maybe,<br>> > the following steps are somewhat wrong, can you help<br>>
> me to point them out?<br>> ><br>> > 1. editconf -f mole.gro -o
out.gro -bt tric -box 5<br>> > 5 10 -angles 90 90 120 -c<br>> >
Should I use the option "-bt tric" here? If not<br>> > triclinic,
possibly, "-bt tric" is wrong.<br>> ><br>> > 2. genbox -cp out -cs
-p topol.top -o b4em.gro<br>> ><br>> > 3. grompp -v -f em -c b4em -p
topol -o box.tpr<br>> ><br>> > 4.trjconv -f b4em.gro -s box.tpr -o
b4em2.gro -ur<br>> > tric -pbc inbox ---- for visualization only.<br>>
> What should my choice for options "-ur & -pbc" in<br>> > this
case?<br>> ><br>> > Urgent equiry and any help will be
greatly<br>> > apprieciated.<br>> ><br>> ><br>> > Xie
Yinghong<br>> > Hong Kong University</p>
</span></div><br>_______________________________________________<br>gmx-users mailing list<br><a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a onclick="return top.js.OpenExtLink(window,event,this)" href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">
http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>Please don't post (un)subscribe requests to the list. Use the<br>www interface or send it to <a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:gmx-users-request@gromacs.org">
gmx-users-request@gromacs.org</a>.<br><br></blockquote></div><br><br clear="all"><br>-- <br><br>Tsjerk A. Wassenaar, M.Sc.<br>Groningen Biomolecular Sciences and Biotechnology Institute (GBB)<br>Dept. of Biophysical Chemistry
<br>University of Groningen<br>Nijenborgh 4<br>9747AG Groningen, The Netherlands<br>+31 50 363 4336<br>