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<DIV><FONT face=Verdana><FONT size=2>Hello everyone,</FONT></FONT></DIV>
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<DIV><FONT face=Verdana><FONT size=2>I am working on a simulation of an infinite
system but I do not know how to build its periodic boundary conditions
in GROMACS. My system is a graphene that is infinite on a
certain direction. Surely I can not generate an infinitely large graphene
for input. So I want to make a finite graphene to repeat along a certain
direction in order to approximate the "infinite" one (e.g: spread the finite
graphene from left to right). But I do not know the technical details. Anyone
have experience on this kind of problems?</FONT></FONT></DIV>
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<DIV><FONT face=Verdana size=2>I have tried to use the PBC in GROMACS, and add
the bonds, angles and dihedrals between atoms on the left edge and atoms on the
right edge and make the size of box to be just the same as the sum of length of
C-C bond and the width(the distance from the left edge to the right edge) of
graphene. But it did not work.</FONT></DIV>
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<DIV><FONT face=Verdana size=2>Anyone can give me some advice? It will be very
helpful.</FONT></DIV>
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<DIV><FONT face=Verdana><FONT size=2>Thanks.</FONT></DIV>
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<DIV><FONT
size=1>___________________________________________________________________________</FONT></DIV>
<DIV><FONT
size=1>___________________________________________________________________________</FONT></DIV>
<DIV><FONT face=Arial size=1></FONT> </DIV>
<DIV><FONT face=Arial size=2><STRONG>Shao Yue</STRONG></FONT></DIV>
<DIV><FONT face=Arial size=2>Institue of Biomechanics and Biomedical
Engineering</FONT></DIV>
<DIV><FONT face=Arial size=2>Department of Engineering Mechanics</FONT></DIV>
<DIV><FONT face=Arial size=2>Tsinghua University</FONT></DIV>
<DIV><FONT face=Arial size=2>P.R. China</FONT></DIV>
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<DIV><FONT
size=1>____________________________________________________________________________</FONT></DIV>
<DIV><FONT
size=1>____________________________________________________________________________</FONT></DIV></DIV>
<DIV><FONT face=Arial
size=1><STRONG></STRONG></FONT> </DIV></FONT></DIV></FONT></DIV></FONT></BODY></HTML>