[gmx-users] bond, angle and dihedral restraints in Gromacs
Mark.Abraham at anu.edu.au
Fri May 22 14:56:30 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
> So, as I understand, they apply RESTRAINTS to the bonds, angles and
Well, they used potential forms similar to those used in restraints. One
can use a harmonic "bond" potential (function type 6 IIRC) in GROMACS
without using a distance restraint. See table 5.4.
> 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?
Section 4.3.2 and Table 5.5 seem to cover it, I think.
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