[gmx-users] bond, angle and dihedral restraints in Gromacs

Rebeca García Fandiño regafan at hotmail.com
Fri May 22 14:09:11 CEST 2009 




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: 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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> -- 
> ========================================
> 
> 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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