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<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>One solution of such problem (similar to
my spin labeled molecule) is that take the center two atoms as dummy atoms,
define a long bond between the two atoms on the rings, Then It is easy to
impose a rotational barrier centered on the long bond.</span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'> </span></font></p>
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<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Regards,</span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Yuguang</span></font></p>
<p class=MsoNormal><font size=3 color=navy face="Times New Roman"><span
style='font-size:12.0pt;color:navy'> </span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Dr. Yuguang Mu</span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>School of Biological Sciences</span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Nanyang Technological University</span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Singapore 637616</span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Tel: 0065-63162885</span></font></p>
<p class=MsoNormal><font size=3 color=navy face="Times New Roman"><span
style='font-size:12.0pt;color:navy'> </span></font></p>
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<p class=MsoNormal style='margin-left:.5in'><font size=2 face=Tahoma><span
style='font-size:10.0pt;font-family:Tahoma'>-----Original Message-----<br>
<b><span style='font-weight:bold'>From:</span></b> gmx-users-bounces@gromacs.org
[mailto:gmx-users-bounces@gromacs.org] <b><span style='font-weight:bold'>On
Behalf Of </span></b>Bamidele Adisa<br>
<b><span style='font-weight:bold'>Sent:</span></b> Thursday, September 16, 2004
10:26 PM<br>
<b><span style='font-weight:bold'>To:</span></b> gmx-users@gromacs.org<br>
<b><span style='font-weight:bold'>Subject:</span></b> [gmx-users] rotational
barrier</span></font></p>
<p class=MsoNormal style='margin-left:.5in'><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'> </span></font></p>
<p class=MsoNormal style='margin-left:.5in'><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'>Hi,<br>
I working with phenylacetylene oligomers in which the phenyl rings are
connected by alkyne linkages.<br>
<img width=131 height=40 src="cid:image001.jpg@01C49C91.F12C74B0"
alt=untitled.bmp><br>
I want to introduce rotation barriers to keep the phenyl rings coplanar. <br>
is it possible to introduce a dihedral around the single bond that connects the
phenyl ring<br>
to the alkyne carbon? if yes, how can i define it in gromacs?<br>
<br>
thanks<br>
dele <br>
<br>
<br>
<br>
<br>
</span></font></p>
<x-sigsep>
<p style='margin-left:.5in'></x-sigsep><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'>______________________<br>
Bamidele Adisa<br>
Dept of Chemical Engineering<br>
Clemson University<br>
Clemson, SC 29634-0909<br>
864-654-0586<br>
______________________</span></font></p>
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