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 <[EMAIL PROTECTED]> 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: [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] > > > 2008-12-05 > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Regards, Yang Ye
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