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<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>
<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">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</P></BODY></HTML>