Re: Re: [gmx-users] how to set up a rigid system
Hi, Constraints could be in the form of bond or direct constraints (often, in Gromacs, bonds are treated as constraints). As shown in http://www.gromacs.org/documentation/reference/online/top.html, you may write top file as following: ; ; Example topology file ; [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 1 1 no 1.0 1.0 ; The force field files to be included #include "rt41c5.itp" [ moleculetype ] ; name nrexcl ABC 3 [ atoms ] ; nrtype resnr residuatomcgnr charge 1 A 1 ABC C1 1 0.683 2 B 1 ABC O2 1 -0.683 3 C 1 ABC N3 2 -0.622 [ bonds ] ; aiaj funct c0 c1 1 2 1 1.00e-01 0.1 2 3 1 1.00e-01 0.1 1 3 1 1.00e-01 0.1 c0 is the distance in nm. for c1, put a relative large value to make it stiff. Yang Ye On Tue, Dec 9, 2008 at 8:56 AM, Xin Liu <[EMAIL PROTECTED]> wrote: > Yang Ye > > I can understand I need to put (3n-6) constraints to the system, but I > don't know how to describe the constraints in the .itp file. Can you give me > a example for the case. > Thank you very much! > -- > Xin Liu > 2008-12-09 > > > -- Regards, Yang Ye ___ gmx-users mailing listgmx-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
Re: [gmx-users] how to set up a rigid system
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/eσ (nm) ε/kb (K) > Geometry > Acetylacetone (Keto) > CH3−0.120.39673.02 > C-C: 0.151 nm, ∠CCCH2: 116.7◦ > > ∠CCO: 123.1◦, ∠CCCH2C: −81.7◦ > C= 0.480.37552.876C-CH2: > 0.152 nm, ∠CCH2C: 111.7◦, > > ∠CCH2CC: −162.1◦ > > O= −0.340.296105.75C=O: > 0.122 nm > -CH2- 0.0 0.390559.42 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= −0.320.296 105.75 > CH3 −0.220.396 73.02 > > Acetylacetone (E) O −0.3660.30085.609 O-C: > 0.133 nm, ∠OCC(H3): 113.6◦ > H(-O-) 0.4110.0 0.0H-O: > 0.099 nm, ∠HOC: 105◦ > C(-OH) 0.3030.37552.876 C-CH3: > 0.150 nm, C=CH: 0.137 nm > CH3−0.1730.39180.573 > ∠CH3C(-O)C: 124.2◦ > CH0.197 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 0.37552.876 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 listgmx-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 ___ gmx-users mailing listgmx-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
[gmx-users] 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/eσ (nm) ε/kb (K) Geometry Acetylacetone (Keto) CH3−0.120.39673.02C-C: 0.151 nm, ∠CCCH2: 116.7◦ ∠CCO: 123.1◦, ∠CCCH2C: −81.7◦ C= 0.480.37552.876C-CH2: 0.152 nm, ∠CCH2C: 111.7◦, ∠CCH2CC: −162.1◦ O= −0.340.296105.75C=O: 0.122 nm -CH2- 0.0 0.390559.42 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= −0.320.296 105.75 CH3 −0.220.396 73.02 Acetylacetone (E) O −0.3660.30085.609 O-C: 0.133 nm, ∠OCC(H3): 113.6◦ H(-O-) 0.4110.0 0.0H-O: 0.099 nm, ∠HOC: 105◦ C(-OH) 0.3030.37552.876 C-CH3: 0.150 nm, C=CH: 0.137 nm CH3−0.1730.39180.573∠CH3C(-O)C: 124.2◦ CH0.197 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 0.37552.876 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 listgmx-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
Re: [gmx-users] how to set up a rigid system
Jinyao Wang wrote: Dear GMX users, I am carrying out MD for a rigid system by Gromacs.But I couldnot know how to set up this rigid system. If you could give me some advice or some material, I will appreciate it. You might try reading in the manual about restraints (position, distance, dihedral) and/or freezegrps (.mdp option). Without a better description of your system, there's not much else I can guess that would help you. -Justin Jinyao Wang [EMAIL PROTECTED] 2008-10-28 ___ gmx-users mailing listgmx-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 -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-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
[gmx-users] how to set up a rigid system
Dear GMX users, I am carrying out MD for a rigid system by Gromacs.But I couldnot know how to set up this rigid system. If you could give me some advice or some material, I will appreciate it. Jinyao Wang [EMAIL PROTECTED] 2008-10-28 ___ gmx-users mailing listgmx-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
