<html><font size="3"><span style="font-family: 宋体;">Hi,gmx users,<br>
</span></font><font size="3"><span class="yC0">I want to set CNT infinite
in the system of CNT and water. </span></font><font size="3"><span
style="font-family: 宋体;">I'm using GMX 4.1,so I have set pbc=xyz,
</span></font><font size="3"><span style="font-family:
宋体;">periodic_molecules=yes in mdp file.<br>
I set the box size larger than CNT's length a C-C bond(half up and half
down).<br>
If I don't do a EM, it will crumble. But if I do it,it can't satisfy
that the box size is larger then CN't length a C-C bond.</span></font><br>
<font size="3"><span class="yC0">I have searched google and gmx mail list,
but still can't solve it</span></font> .<font size="3"><span
style="font-family: 宋体;"><br>
<br>
I found that GMX online document about Carbon Nanotube(</span></font><font
size="3"><span style="font-family: 宋体;"><a
href="http://www.gromacs.org/index.php?title=Documentation/How-tos/Carbon_Nanotube">http://www.gromacs.org/index.php?title=Documentation/How-tos/Carbon_Nanotube</a>)<br>
say,<br>
<br>
</span></font><span style="font-style: italic;">Be absolutely sure that the
"terminal" carbon atoms are sharing a bond in the topology
file.</span><font size="3"><span style="font-family: 宋体;"><br>
<br>
I don't understand it.How should I do?<br>
<br>
Thanks!<br>
</span></font><br>
<font size="3"><span style="font-family: 宋体;"></span></font><font
size="3"><span style="font-family: 宋体;"></span></font></html>