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<p class=MsoNormal style='text-autospace:none'><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'>>x2top -h<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'>>Did you use the -alldih flag?
For OPLS like force field all dihedrals are need, for gromos like ff only one
dihedral per bond is kept, that is >why.<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'>Thanks, David. I did not use –alldih.
After I used it, four dihedrals for one bond are all kept. Anyway I have got this
point about the difference of defining dihedral between OPLS and Gromos ff,
though I still don’t clearly understand why difference exists.<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'>>David van der Spoel, Ph.D.,
Professor of Biology<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'>>Molec. Biophys. group, Dept. of
Cell & Molec. Biol., <st1:place w:st="on"><st1:PlaceName w:st="on">Uppsala</st1:PlaceName>
<st1:PlaceType w:st="on">University</st1:PlaceType></st1:place>.<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'>>Box 596, 75124 <st1:place w:st="on"><st1:City
w:st="on">Uppsala</st1:City>, <st1:country-region w:st="on">Sweden</st1:country-region></st1:place>.
Phone: +46184714205. Fax:
+4618511755.<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'>>spoel@xray.bmc.uu.se spoel@gromacs.org
<a href="http://folding.bmc.uu.se/">http://folding.bmc.uu.se</a><o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'>Zhongqiao Hu<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'>Dept of Chem & Biomol Engineer<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'>National Univ of <st1:country-region
w:st="on"><st1:place w:st="on">Singapore</st1:place></st1:country-region><o:p></o:p></span></font></p>
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12.0pt'><o:p> </o:p></span></font></p>
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