<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
<HTML><HEAD>
<META http-equiv=Content-Type content="text/html; charset=gb2312">
<META content="MSHTML 6.00.2900.2722" name=GENERATOR></HEAD>
<BODY>
<P>Dear Dr. Tsjerk:</P>
<P> </P>
<P>Many many thanks for your detailed explanation. I am trying it
later although it is difficult for me. </P>
<P> </P>
<P>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?</P>
<P> </P>
<P>Breifly, I just want to be made sure about the following two things:</P>
<P> </P>
<P>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?</P>
<P> </P>
<P>2. While using "editconf" to generate the box, the option "-bt tric" is
necessary in my case?</P>
<P> </P>
<P>Thanks, if not mind, please give me direct answers about the two
questions above.</P>
<P> </P>
<P>Thanks again.</P>
<P> </P>
<P> </P>
<P>Xie Yinghong</P>
<P>Hong Kong University</P>
<P> </P>
<P> </P>
<P>>Hi Xie Yinghong,</P>
<P>>Since one of your vectors is exactly perpendicular to the other two,
lets<BR>>just focus on the base. And remember that what goes in 2D counts in
3D too.<BR>>Your base is a parallelogram with angles of 120 and 60 degrees.
Now copy<BR>>that several times. Then take one of the corner points in the
centre. Draw<BR>>lines to mark the borders where any point in the plane lies
closer to that<BR>>point than to any of the other corner points. You will get
a marked shape,<BR>>which is generally called the Voronoi region. In your
case, you'll find that<BR>>the Voronoi region of your system is a perfect
hexagon. With your third<BR>>vector, you'll have a perfectly regular
hexagonal prism.</P>
<P>>Now if you do it for the other points two, you'll find that the same
hexagon<BR>>will be located at each corner point in the grid created by the
copied<BR>>parallelograms. Thus, you can equally well look at your system as
an<BR>>infinite replicated system of hexagons. These will be connected by the
edges<BR>>of the original unit cells. Imagine the first vector aligned with
the<BR>>x-axis, and the central corner point at the origin (thus with one
hexagon<BR>>centred at the origin) and you'll have one neighbouring hexagon
at +1x. Now<BR>>you defined your second vector to have an angle of 120
degrees. So in your<BR>>case you'll take the second hexagon at -0.5x,
+0.866y. But if you look at<BR>>the copied system, you'll find that there's
also a hexagon at +0.5x,<BR>>+0.866y. That's equally valid to take as a
second copy, and if you draw a<BR>>line connecting from the origin to that,
it will have an angle of 60 degrees<BR>>with the positive x-axis. In other
words, with an angle of 60 degrees (and<BR>>equal vector lengths) you have
defined the exact same infinite simulation<BR>>system.</P>
<P>>I encourage you to draw the things I explained above. Also google
for<BR>>'lattice', 'voronoi', 'triclinic' and do have a look at the paper of
Bekker<BR>>I suggested before.</P>
<P>>I hope this helps,</P>
<P>>Tsjerk</P>
<P>>On 10/14/05, Yinghong <<A
href="mailto:xieyh@hkusua.hku.hk">xieyh@hkusua.hku.hk</A>>
wrote:<BR>><BR>> Dear Tsjerk:<BR>><BR>> Thanks for your kind
help. And, I need furthur confirmation about the<BR>> following
things.<BR>><BR>> My box is actually based on hexagonal prism, but
its cross-section is not<BR>> a hexagon. In fact, it is only a monoclinic
cell totoally with 6 faces in<BR>> the whole box, instead of 8 faces in
hexagonal prism. Accordingly, is my<BR>> previous definition
correct?<BR>><BR>> So, in such case, I used "editconf -bt tric" to build
the box, is that<BR>> ok????? As told by you, all the box types are the same
for simulation, to<BR>> this point, I need your confirmation,
thanks.<BR>><BR>> By the way, what is the meaning of the third angle equal
to 60 degree? I<BR>> searched many previous achieves, 120 degree was always
adopted.<BR>><BR>> Xie Yinghong<BR>><BR>> HongKong
University<BR>><BR>> >Hi Yinghong,<BR>><BR>>
> I believe you want to set up a hexagonal prism according to your<BR>>
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<BR>> -ur<BR>> >and compare the results, keeping in
mind that it's all the same system,<BR>> but<BR>> >just different
representations (interconversion of box types).<BR>><BR>> >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<BR>>
think<BR>> >of it, you may as well set the third angle to 60 degrees. That
will give<BR>> the<BR>> >same box :p (that will describe the same
lattice), but is more likely to<BR>> >comply to Gromacs prerequisites for
boxes.<BR>><BR>> >Cheers,<BR>><BR>>
>Tsjerk<BR>><BR>><BR>> On 10/13/05, Rodrigo Reston <<A
href="mailto:rodrigoreston@yahoo.com.br">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">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<BR>></P></BODY></HTML>