Hi Yinghong,<br>
<br>
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). <br>
<br>
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.<br>
<br>
Cheers,<br>
<br>
Tsjerk<br>
<br><br><div><span class="gmail_quote">On 10/13/05, <b class="gmail_sendername">Rodrigo Reston</b> <<a href="mailto:rodrigoreston@yahoo.com.br">rodrigoreston@yahoo.com.br</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;">
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
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</a>.<br><br><br><br><br><br>__________________________________<br>Yahoo! Mail - PC Magazine Editors' Choice 2005<br><a href="http://mail.yahoo.com">http://mail.yahoo.com</a><br>_______________________________________________
<br>gmx-users mailing list<br><a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://www.gromacs.org/mailman/listinfo/gmx-users">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 href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<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>