[gmx-users] how to set up rigid system for acetylacetone

Xin Liu yjqqliu at 163.com
Fri Dec 5 08:13:34 CET 2008


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     charge:q/e    LJ core diameter(nm)  depth well/kb (K)          Geometry
Acetylacetone (Keto)   
                       CH3         -0.12          0.396              73.02                C-C: 0.151 nm, angle:CCCH2: 116.7 degree   
                                                                               angle:CCO: 123.1degree , dihedral angle CCCH2C: -81.7degree 
                       C=           0.48          0.375             52.876               C-CH2: 0.152 nm, angle: CCH2C: 111.7 degree ,
                                                                                    dihedral angle:CCH2CC: -162.1 degree 
 
                       O=          -0.34         0.296              105.75                      C=O: 0.122 nm
                     -CH2-          0.0          0.3905             59.42                    CH2-C: 0.153 nm, angle: CH2CO: 122.0 degree
                                                                                               angle:CH2CC: 115.4 degree
                      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 (Enpl)      O           -0.366         0.300             85.609          O-C: 0.133 nm, angle: OCC(H3): 113.6 degree
                       H(-O-)       0.411           0.0              0.0                          H-O: 0.099 nm, angle: 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                      angle: CH3C(-O)C: 124.2 degree
                       CH         0.197           0.380         57.912                    angle: CC(H)C: 120.5 degree, CC(=O): 0.145nm,
                                                                               angle: C(H)C=O: 121.6 degree, angle: CC(=O)CH3: 121.6 degree
                       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!

 
 
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 
 				

2008-12-05








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