[gmx-users] Contraints on both angles and dihedrals

[Mark Abraham]

Hi,

Of what would that be a good physical model?

Mark

On Wed, May 9, 2018, 10:07 Ahmet Yildirim <ahmedo047 at gmail.com> wrote:

> Hi,
>
> With stiff restraints using standard GROMACS versions I couldn't get what
> I want. If Developers implement some like this:
> contraints-grps = ligand
> constrains = all-bonds all-angles all-dihedrals
>
> it would be wonderful :)
>
> > On 9 May 2018, at 10:56, Felipe Merino <
> felipe.merino at mpi-dortmund.mpg.de> wrote:
> >
> > Hi,
> >
> > I guess you can always get a similar final result using some stiff
> restraints with gromacs/plumed.
> >
> > Best
> >
> > Felipe
> >
> >
> >> On 09/05/18 09:48, Ahmet Yildirim wrote:
> >> Hi,
> >>
> >> I am facing with the same problem... Unfortunately GROMACS does not have
> >> the capability to constraint all the internal coordinates (bond lengths,
> >> bond angles and dihedral angles) of a certain group (e.g. ligand) in the
> >> simulation system. Hope that Developers will take into consideration the
> >> implementation of such a feature to the next version :)
> >>
> >>
> >>
> >>> On 8 May 2018 at 14:23, Mark Abraham <mark.j.abraham at gmail.com> wrote:
> >>>
> >>> Hi,
> >>>
> >>> There is no general support for rigid body dynamics in GROMACS.
> >>>
> >>> Mark
> >>>
> >>>> On Tue, May 8, 2018, 12:52 Qasim Pars <qasimpars at gmail.com> wrote:
> >>>>
> >>>> Dear users,
> >>>>
> >>>> I would like to constraint all the angles and dihedrals of a ligand to
> >>>> make it rigid but Gromacs does not have this capability for the
> >>> dihedrals.
> >>>> However, the angle and dihedral restraints do not make it rigid as I
> >>> want,
> >>>> as it is very flexible.
> >>>>
> >>>> Do you have an idea on how I can make the ligand rigid using gromacs?
> >>>>
> >>>> Thanks in advance,
> >>>> --
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> >>
> >>
> >
> > --
> > Felipe Merino,
> > Max Planck Institute for Molecular Physiology
> > Department of Structural Biochemistry
> > Otto-Hahn-Str. 11
> > 44227 Dortmund
> > Phone: +49 231 133 2307
> >
> > ORCID:  https://orcid.org/0000-0003-4166-8747
> > Publons: https://publons.com/a/1305699/
> > Researchgate: https://www.researchgate.net/profile/Felipe_Merino
> >
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