Thank you very much for the suggestion. Actually, I am trying to reproduce the results from another publication (JACS 2005, 127, 7166) http://pubs.acs.org/doi/full/10.1021/ja050044d where they used Gromacs/amber to simulate a CNT. They apply: "Carbon−carbon bond lengths of 0.14 nm and bond angles of 120° were maintained by harmonic potentials with spring constants of 393 960 kJ mol-1 nm-2 and 527 kJ mol-1 deg-2 before relaxation. In addition, a weak dihedral angle potential was applied to bonded carbon atoms." So, as I understand, they apply RESTRAINTS to the bonds, angles and dihedrals. I have tried to construct the [distance_restraints] for my system (I show you here a little part): [ distance_restraints ] ; atom1 atom2 type index type2 low up1 up2 fac 1 310 1 1 1 0.142 0.146 0.150 1.0 2 290 1 2 1 0.142 0.146 0.150 1.0 3 291 1 3 1 0.142 0.146 0.150 1.0 (...) but I don' t understand very well which value should I write for "low up1 up2". The manual says that "the columns low, up1 and up2 hold the values of r0 , r1 and r2 from eqn. 4.76", but looking at this equation I still don' t understand which should be the better values for my case. I have looked into the mail archive, and some other people asked for that, but I did not find any proper solution. How could I choose the best values for "low up1 up2" to restrain my bond values to 1.42 Amstrong? The other question is about angle restraints, I have found indications in the wiki of how to treat the dihedral restraints (http://wiki.gromacs.org/index.php/Dihedral_Restraints), however I did not find any similar for the angle restraints. I have seen in the mail archive that 2 pairs of atoms should be used, but I did not find anything to trust in. Could you please give me some indications of how to treat angle restraints? Thank you very much, Best wishes, Rebeca Garcia Parc Cientific de Barcelona Spain > Date: Thu, 21 May 2009 12:41:57 -0400 > From: [email protected] > To: [email protected] > Subject: Re: [gmx-users] bond, angle and dihedral restraints in Gromacs > > > > Rebeca García Fandiño wrote: > > Hello, > > I would like to simulate a CNT and I want to apply a harmonic potential: > > -on the C-C bonds > > -on the bond angles > > -on the dihedral angles > > with a different spring constant for each case. > > > > I have read Section 4.3 from Gromacs manual, but I actually have some > > doubts about how to include this in the topology. > > > > -for the distance restraints I have tried to use genrestr: > > > > genrestr -f cnt_wat_gmx_centered.gro -o posre_dist.itp -disre -fc 400000 > > > > The file I obtain is something like: > > > > ; distance restraints for UNK of cnt_wat_gmx.gro created by > > rdparm2gmx.pl Wed May 20 10:20:59 BST 2009 > > > > [ distance_restraints ] > > ; i j ? label funct lo up1 up2 weight > > 1 2 1 0 1 0.403354 0.603354 1.60335 1 > > 1 3 1 1 1 0.587676 0.787676 1.78768 1 > > 1 4 1 2 1 0.769212 0.969212 1.96921 1 > > 1 5 1 3 1 0.86081 1.06081 2.06081 1 > > (...) > > > > This is different from the [distance_restraint] example shown in pag 69 > > of the manual, now I don' t have the fac column. I would like to apply a > > The format of the distance_restraints section appears correct. If you read > the > description of the "fac" column, it is a weighting factor for that particular > restraint. So therefore, "weight" is probably equivalent. > > > spring constant of 400000 to C-C bonds, but where is the constant here? > > How could I apply a determined spring constant? In the .mdp file? > > Besides, all the distances are restrained... Is there any way to > > restrain only the C-C bonds? I mean I don' t want to restrain the > > distance between a carbon and a carbon far away from it, only > > restraining the neighbouring carbons to a distance of 1.4 A. > > > > You cannot use genrestr for this purpose. Using genrestr -disre generates a > matrix of all atoms you specify. Also, -fc is expected to be used with > position > restraints; note the format given in genrestr -h. > > Are you really interested in applying restraints to all bonds, angles, > dihedrals, and distances? Realize that constraints (Section 5.5) and > restraints > are separate ideas in Gromacs. > > If you want to define your own force constants for bonds, angles, etc. simply > do > so in the topology yourself (Table 5.4). > > -Justin > > > Another question is: Is there any tool to construct the equivalent > > angle_restraints and dihedral_restraints in an authomatic way, or should > > I do it by hand? > > > > Thank you very much in advance for your help. > > > > Best wishes, > > > > Dr. Rebeca Garcia > > Parc Cientific de Barcelona > > Spain > > > > > > > > > > > > > > ------------------------------------------------------------------------ > > Haz búsquedas con Live Search, ¡todas tus búsquedas tienen premio! > > <http://www.buscalasuerte.com/> > > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > gmx-users mailing list [email protected] > > 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 > Ph.D. Candidate > ICTAS Doctoral Scholar > 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 list [email protected] > 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 _________________________________________________________________ Comparte, crea, disfruta… Descubre todo, en estos vídeos http://www.windowslive.es
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