Xie Yinghong,<br>
<br>
It's okay, apparently I'm failing in making myself clear. I've dug up
this image which visualizes the interconversion of box types. You see a
molecule (blue) in a hexagonal unit cell (yellow). The centres of these
unitcells are connected by the black lines, which form the lattice. One
cell, contained by four lattice points, is exactly equal in volume and
composition as the original hexagonal unit cell. I hope this is clear
now.<br>
<br>
But we've wandered a long way, and if I'm not mistaken your simulations
crashed, and you thought it had to do with the box. Now, understanding
how periodic boundaries work, the infinite simulation system and the
interconversion of box types is important in MD, I think it does not
solve your problem. It would only clear you of the misconception that
it had to do with your box being triclinic. The cause of the crash is
not related to the nature of the box, unless you've set it to be too
small to contain your entire system.<br><br>
Tsjerk<br>
<br><div><span class="gmail_quote">On 10/15/05, <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 Dr. Tsjerk:</p>
<p> </p>
<p>Firstly, sorry to occupy you so much time to deal with my questions, thanks
again.</p>
<p> </p>
<p>But, I do not know why you always mentioned about a hexagonal prism and why I
need to make such a transformation from parallelogram to hexagon.</p>
<p> </p>
<p>The box I need is only a parallelogram one. As a fact, I can get such a box
through defining "angles=90 90 120" in editconf command, and a parallelogram
shape box can be seen by trjconv. So, I can not understand why hexagon is always
mentioned?</p>
<p> </p>
<p>Thanks and regards,</p><span class="sg">
<p> </p>
<p>Yinghong</p>
<p>Hong Kong University</p></span><div><span class="e" id="q_106ef3a33af89bb2_2">
<p> </p>
<p>>You just don't get it... Now find and read the paper of Bekker and do
the<br>>excercise from the previous mail. The answers are:<br><br>>1. Your
parallelogram can be transformed to a single hexagonal prism with<br>>exactly
the same lattice vectors, volume and content. One to one.<br><br>>2. I think
that when setting the box with -vectors and -angles, -bt tric
is<br>>implicit, but it doesn't hurt
anyway.<br><br>>Tsjerk<br></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">
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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>