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<DIV><FONT face=Verdana color=#000000 size=2>Thanks, Mark</FONT></DIV>
<DIV><FONT face=Verdana size=2></FONT> </DIV>
<DIV><FONT face=Verdana size=2>I am so sorry about my failure to describe my
problem clearly. My problem is that while I was doing EM with that infinite
system, the Fmax was unreasonably large (~1e4). But just now, I changed the
pbc=xyz to pbc=full in my em.mdp file, then it is OK now. </FONT></DIV>
<DIV><FONT face=Verdana size=2>So I have a new question now: as the pbc=full has
never been mentioned in GROMACS 3.3 manual, what is the difference between
pbc=full and pbc=xyz?</FONT></DIV>
<DIV><FONT face=Verdana size=2></FONT> </DIV>
<DIV><FONT face=Verdana size=2>I have checked the example of CNT on the website
you mentioned. I do not use x2top in my simulation, because I generate the input
.gro and .itp files directly with other programs. I manually add the
topology among atoms on the neighboring edges of graphene and its
image. But the pbc=full mentioned in that example is very
helpful. </FONT></DIV>
<DIV><FONT face=Verdana size=2></FONT> </DIV>
<DIV><FONT face=Verdana size=2>Thanks for your suggestion!</FONT></DIV>
<DIV><FONT face=Verdana size=2></FONT> </DIV>
<DIV align=left>
<DIV align=left><FONT face=Verdana size=2>
<HR style="WIDTH: 122px; HEIGHT: 2px" SIZE=2>
</FONT></DIV>
<DIV><FONT color=#c0c0c0><FONT face=Verdana size=2>silvester.thu</FONT></DIV>
<DIV><FONT face=Verdana size=2>2008-05-15</FONT></FONT></DIV></DIV>
<DIV><FONT face=Verdana size=2>
<HR>
</FONT></DIV>
<DIV><FONT face=Verdana><FONT size=2><STRONG>发件人：</STRONG> Mark
Abraham</FONT></FONT></DIV>
<DIV><FONT face=Verdana><FONT size=2><STRONG>发送时间：</STRONG>
2008-05-15 10:29:49</FONT></FONT></DIV>
<DIV><FONT face=Verdana><FONT size=2><STRONG>收件人：</STRONG> Discussion list for
GROMACS users</FONT></FONT></DIV>
<DIV><FONT face=Verdana><FONT size=2><STRONG>抄送：</STRONG> </FONT></FONT></DIV>
<DIV><FONT face=Verdana><FONT size=2><STRONG>主题：</STRONG> Re: [gmx-users] how to
build the input files of an infinite system</FONT></FONT></DIV>
<DIV><FONT face=Verdana size=2></FONT> </DIV>
<DIV><FONT face=Verdana size=2>
<DIV>silvester.thu wrote:</DIV>
<DIV>> Hello everyone,</DIV>
<DIV>> </DIV>
<DIV>> I am working on a simulation
of an infinite system but I do
not know how </DIV>
<DIV>> to build its periodic boundary
conditions in GROMACS. My system is a
</DIV>
<DIV>> graphene that is infinite on a
certain direction. Surely I can not
</DIV>
<DIV>> generate an infinitely large graphene
for input. So I want to make a
</DIV>
<DIV>> finite graphene to repeat along a
certain direction in order to </DIV>
<DIV>> approximate the "infinite" one (e.g:
spread the finite graphene from </DIV>
<DIV>> left to right). But I do not
know the technical details. Anyone have
</DIV>
<DIV>> experience on this kind of
problems?</DIV>
<DIV> </DIV>
<DIV>Yes. You can probably adapt the advice
here</DIV>
<DIV><A
href="http://wiki.gromacs.org/index.php/Carbon_Nanotube">http://wiki.gromacs.org/index.php/Carbon_Nanotube</A>
to your needs.</DIV>
<DIV> </DIV>
<DIV>> I have tried to use the PBC
in GROMACS, and add the bonds, angles
and </DIV>
<DIV>> dihedrals between atoms on the
left edge and atoms on the right
edge and </DIV>
<DIV>> make the size of box to be
just the same as the sum of
length of C-C </DIV>
<DIV>> bond and the width(the distance
from the left edge to the right
edge) of </DIV>
<DIV>> graphene. But it did not
work.</DIV>
<DIV>> </DIV>
<DIV>> Anyone can give me some advice?
It will be very helpful.</DIV>
<DIV> </DIV>
<DIV>Describing failure with "It did not
work" makes it impossible for us
to</DIV>
<DIV>give free advice at a rate that
is worth our time. A detailed</DIV>
<DIV>description of what you did and what
happened is almost always much more</DIV>
<DIV>valuable and a better use of
everybody's time than the alternative
:-)</DIV>
<DIV>See the advice here <A
href="http://wiki.gromacs.org/index.php/Support">http://wiki.gromacs.org/index.php/Support</A></DIV>
<DIV> </DIV>
<DIV>Mark</DIV>
<DIV>_______________________________________________</DIV>
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