2008-12-05
刘鑫
发件人： 刘鑫
发送时间： 2008-12-05 11:30:41
收件人： [EMAIL PROTECTED]
抄送：
主题： help: how to set up a rigid system
Dear GMX users,
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.
Model parameters
Molecule Site q/e σ (nm) ε/kb (K) Geometry
Acetylacetone (Keto)
CH3 −0.12 0.396 73.02 C-C: 0.151
nm, ∠CCCH2: 116.7◦
∠CCO: 123.1◦, ∠CCCH2C: −81.7◦
C= 0.48 0.375 52.876 C-CH2: 0.152
nm, ∠CCH2C: 111.7◦,
∠CCH2CC: −162.1◦
O= −0.34 0.296 105.75 C=O: 0.122 nm
-CH2- 0.0 0.3905 59.42 CH2-C:
0.153 nm, ∠CH2CO: 122.0◦
∠CH2CC: 115.4◦
C= 0.52 0.375 52.876 C=O:
0.122 nm, C-CH3: 0.151 nm
O= −0.32 0.296 105.75
CH3 −0.22 0.396 73.02
Acetylacetone (E) O −0.366 0.300 85.609 O-C: 0.133
nm, ∠OCC(H3): 113.6◦
H(-O-) 0.411 0.0 0.0 H-O:
0.099 nm, ∠HOC: 105◦
C(-OH) 0.303 0.375 52.876 C-CH3:
0.150 nm, C=CH: 0.137 nm
CH3 −0.173 0.391 80.573 ∠CH3C(-O)C:
124.2◦
CH 0.197 0.380 57.912 ∠CC(H)C:
120.5◦, C C( O): 0.145nm,
∠C(H)C=O: 121.6◦, ∠CC(=O)CH3: 121.6◦
C(=O) 0.360 0.375 52.876 C=O: 0.125
nm, CCH3: 0.151 nm
CH3 −0.258 0.391 80.573
O= −0.474 0.296 105.75
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!
2008-12-05
Dr. Xin Liu,
School of Chemistry and Chemical Engineering
Sun Yat-Sen University
No.135, Xingang Xi Road,
Guangzhou, 510275
P. R. China
Tel.: +86-20-84115559
Fax: +86-20-84112245
E-mail: [EMAIL PROTECTED] mailto:[EMAIL PROTECTED]
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