[gmx-users] help: how to set up a rigid system

[刘鑫]

2008-12-05



刘鑫



发件人： 刘鑫
发送时间： 2008-12-05 11:30:41
收件人： gmx-users-request at gromacs.org
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: liuxin23 at mail.sysu.edu.cn mailto:liuxin23 at mail.sysu.edu.cn
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