<!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 Yang Ye:</P>
<P> </P>
<P>The PBC I used is one particular tpye of cubic box, which cross-section
is a rhombus instead of rectangle.</P>
<P>As we know, a hexagon can be divided into three rhombus, ok? We call it as
unit cell, which is the box I employed. Normally, some distance is existing
between solute molecule and box boundary in most simulations. But in my
simulated box, the boudary is initially tangent to the solute, which means there
is almost no distance between solute and box boundary. As you said, if your DNA
exceed the boundary, one part will be in the right side, and the other will
emergy in the left side. This is also the case I often encountered.</P>
<P>In my simulation, the solute is a nanotube, as the simulation, the tube will
be outside the box and broken into several parts. And finally, the run will be
stopped possibly due to the broken nanotube.</P>
<P> </P>
<P>><EM> but Gromacs told me that has no effect for unit cell
representation.<BR></EM>which will be told when I use "trjconv -ur tric -pbc
whole (not inbox)" to define a tric box. Do you know how to
define a tric box as I mentioned before?</P>
<P> </P>
<P>Thanks for your help and discussion.</P>
<P> </P>
<P>Xie Yinghong</P>
<P>Hong Kong University.</P>
<P><BR><BR>><I> Dear users:<BR></I>><I><BR></I>><I> In my system, I
chose a triclinc box (monoclinic cell) as my periodic<BR></I>><I> boundary
condition, which is defined as follows:<BR></I>><I><BR></I>><I> editconf
-f *.pdb -o -bt tric -box 5 5 10 -angles 90 90 120 -c<BR></I>><I> genbox -cp
out -cs -p topol -o b4em<BR></I>><I> grompp -v -f em -c b4em -p topol -o
box<BR></I>><I> trjconv -f b4em -s box -o b4em2.gro -ur tric -pbc
inbox<BR></I>><I><BR></I>><I> If I used "-pbc inbox", my simulated
molecule would be broken.<BR></I>><I><BR></I>What do you mean by "broken"? In
my simulation, molecule will gradually<BR>slide to the boundary of the box and
even move out from it. But at long<BR>as it is still kept at a good shape, there
is no impact to MD<BR>simulation. For DNA, there could be case that one strand
on the left<BR>boundary and another on the right boundary. A awk script or
program will<BR>do the trick and make analysis proceeding.<BR><BR>><I> And,
if "-pbc whole" was adapted, the molecule could be kept intact,<BR></I>><I>
but Gromacs told me that has no effect for unit cell
representation.<BR></I>><I><BR></I>where did this "gromacs told me..." come
from?<BR><BR>><I> In my simulations, I empolyed "-pbc whole" in order to keep
molecule<BR></I>><I> intact, but after ~200ps simulation, mdrun is
interrupted, and the<BR></I>><I> initial intact molecule is also broken at
this moment.<BR></I>><I><BR></I>Also, what do you mean "broken"
here?<BR><BR>><I> So, Could you tell me that the way I defined a triclinc box
*(not<BR></I>><I> hexagonal box)* is right?<BR></I>><I><BR></I>><I>
Which option should I choose in "trjconv" for -ur and
-pbc?<BR></I>><I><BR></I>><I> What made my simulation
stopped?<BR></I>><I><BR></I>><I> Because this is my first time using
triclinc box, many things are very<BR></I>><I> strange for
me.<BR></I>><I><BR></I>><I> Any help is
appreciated.<BR></I>><I><BR></I>><I> Xie
Yinghong<BR></I>><I><BR></I>><I> Hong Kong
University<BR></I>><I><BR></I>><I>------------------------------------------------------------------------<BR></I>><I><BR></I>><I>_______________________________________________<BR></I>><I>gmx-users
mailing list<BR></I>><I><A
href="http://www.gromacs.org/mailman/listinfo/gmx-users">gmx-users at
gromacs.org</A><BR></I>><I><A
href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</A><BR></I>><I>Please
don't post (un)subscribe requests to the list. Use the <BR></I>><I>www
interface or send it to <A
href="http://www.gromacs.org/mailman/listinfo/gmx-users">gmx-users-request at
gromacs.org.</A><BR></I>><I><BR></P></I></BODY></HTML>