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: [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
------------------------------------------------------------------------
Más rápido, fácil, seguro y con lo que más te gusta de Windows Live, así
es el nuevo Internet Explorer 8 ¡Descárgatelo!
<http://ie8.msn.com/microsoft/internet-explorer-8/es-es/ie8.aspx>
--
========================================
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
