[gmx-users] Contraints on both angles and dihedrals

[Felipe Merino]

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