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<DIV><FONT face=Verdana color=#000080 size=2><SPAN
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<DIV><FONT face=Verdana color=#000080 size=2></FONT> </DIV>
<DIV><FONT face=Verdana color=#c0c0c0 size=2>2008-12-05</FONT></FONT></DIV>
<DIV align=left>
<DIV align=left><FONT face=Verdana size=2>
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<DIV><FONT color=#c0c0c0><FONT face=Verdana
size=2><SPAN>刘鑫</SPAN></FONT></DIV></DIV>
<DIV><FONT face=Verdana size=2>
<HR>
</FONT></DIV>
<DIV><FONT face=Verdana><FONT size=2><STRONG>发件人：</STRONG>
刘鑫</FONT></FONT></DIV>
<DIV><FONT face=Verdana><FONT size=2><STRONG>发送时间：</STRONG>
2008-12-05 11:30:41</FONT></FONT></DIV>
<DIV><FONT face=Verdana><FONT size=2><STRONG>收件人：</STRONG>
gmx-users-request@gromacs.org</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> help: how to set up a
rigid system</FONT></FONT></DIV>
<DIV><FONT face=Verdana size=2></FONT> </DIV>
<DIV><FONT face=Verdana size=2>
<DIV> </DIV>
<DIV>Dear GMX users,</DIV>
<DIV> </DIV>
<DIV> </DIV>
<DIV>I am carrying out MD simulation of acetylacetone by Gromacs. As we know, there are keto and enol two tautomers for acetylacetone. The tautomers were treated as rigid species in the literature (Y.K. Park, C. H. Turner, J. Supercrit. Fluids 37 (2006) 201–208)). The parameters of the LJ interactions and the electrostatic interactions of keto and enol models for acetylacetone and their equilibrium geometry were given. Dihedral angles are included in the models to specify the keto geometry, while the enol form is calculated to be a planar molecule. </DIV>
<DIV> </DIV>
<DIV> Model parameters </DIV>
<DIV>Molecule Site q/e σ (nm) ε/kb (K) Geometry</DIV>
<DIV>Acetylacetone (Keto) </DIV>
<DIV>
CH3 −0.12 0.396 73.02 C-C: 0.151 nm, ∠CCCH2: 116.7◦ </DIV>
<DIV> ∠CCO: 123.1◦, ∠CCCH2C: −81.7◦</DIV>
<DIV> C= 0.48 0.375 52.876 C-CH2: 0.152 nm, ∠CCH2C: 111.7◦,</DIV>
<DIV>
∠CCH2CC: −162.1◦</DIV>
<DIV> </DIV>
<DIV> O= −0.34 0.296 105.75 C=O: 0.122 nm</DIV>
<DIV> -CH2- 0.0 0.3905 59.42 CH2-C: 0.153 nm, ∠CH2CO: 122.0◦</DIV>
<DIV>
∠CH2CC: 115.4◦</DIV>
<DIV> C= 0.52 0.375 52.876 C=O: 0.122 nm, C-CH3: 0.151 nm</DIV>
<DIV> O= −0.32 0.296 105.75</DIV>
<DIV> CH3 −0.22 0.396 73.02</DIV>
<DIV> </DIV>
<DIV>Acetylacetone (E) O −0.366 0.300 85.609 O-C: 0.133 nm, ∠OCC(H3): 113.6◦</DIV>
<DIV> H(-O-) 0.411 0.0 0.0 H-O: 0.099 nm, ∠HOC: 105◦</DIV>
<DIV> C(-OH) 0.303 0.375 52.876 C-CH3: 0.150 nm, C=CH: 0.137 nm</DIV>
<DIV> CH3 −0.173 0.391 80.573 ∠CH3C(-O)C: 124.2◦</DIV>
<DIV> CH 0.197 0.380 57.912 ∠CC(H)C: 120.5◦, C C( O): 0.145nm,</DIV>
<DIV>
∠C(H)C=O: 121.6◦, ∠CC(=O)CH3: 121.6◦</DIV>
<DIV> C(=O) 0.360 0.375 52.876 C=O: 0.125 nm, CCH3: 0.151 nm</DIV>
<DIV> CH3 −0.258 0.391 80.573</DIV>
<DIV> O= −0.474 0.296 105.75 </DIV>
<DIV> </DIV>
<DIV> </DIV>
<DIV> But I could not know how to set up this rigid system in gromacs. If you could give me some advice or some material, I will appreciate it. Thank you!</DIV>
<DIV>2008-12-05 </DIV>
<DIV> </DIV>
<DIV> </DIV>
<DIV>Dr. Xin Liu,</DIV>
<DIV> </DIV>
<DIV>School of Chemistry and Chemical Engineering</DIV>
<DIV> </DIV>
<DIV>Sun Yat-Sen University</DIV>
<DIV> </DIV>
<DIV>No.135, Xingang Xi Road,</DIV>
<DIV> </DIV>
<DIV>Guangzhou, 510275</DIV>
<DIV> </DIV>
<DIV>P. R. China</DIV>
<DIV> </DIV>
<DIV>Tel.: +86-20-84115559</DIV>
<DIV> </DIV>
<DIV>Fax: +86-20-84112245</DIV>
<DIV> </DIV>
<DIV>E-mail: liuxin23@mail.sysu.edu.cn mailto:liuxin23@mail.sysu.edu.cn</DIV></FONT></DIV></FONT></BODY></HTML>