[gmx-users] Contraints on both angles and dihedrals

[Ahmet Yildirim]

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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