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

[Yang Ye]

To set up rigid system, you need to put (3n-6) constraints (in the form of
bond, angle), where n is the atom/bead (in the case of coarse-grain model)
number in the molecule.

YY

On Fri, Dec 5, 2008 at 1:03 PM, Xin Liu <yjqqliu at 163.com> wrote:

> 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!
>
>
>
> 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
>
>
> 2008-12-05
>
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-- 
Regards,
Yang Ye
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