[gmx-users] bond, angle and dihedral restraints in Gromacs
Justin A. Lemkul
jalemkul at vt.edu
Fri May 22 14:18:44 CEST 2009
Rebeca García Fandiño wrote:
> 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.^"
>
A harmonic potential is simply defined as bond type 1 (manual section 4.2.1),
and similarly for angles (section 4.2.5). For the bonds, you can specify, i.e.:
[ bonds ]
1 2 1 0.14 393960
Note that Gromacs uses kJ mol^-1 rad^-2 for angle force constants. The
information about the dihedrals is vague, so I can't make any suggestion there.
> 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?
>
These are distances that determine the restoring force to maintain a distance.
Figure 4.13 is perhaps a bit more illustrative of how they should be
interpreted, but again I don't believe that you will need distance restraints to
apply a simple harmonic potential.
-Justin
> 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: jalemkul at vt.edu
> > To: gmx-users at gromacs.org
> > 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
> > >
> > >
> > >
> > >
> > >
> > >
> > >
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> > >
> > >
> > >
> ------------------------------------------------------------------------
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> > --
> > ========================================
> >
> > 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
> >
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--
========================================
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
========================================
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