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 <[email protected]> > 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 <[email protected]> wrote: >>> >>> Hi, >>> >>> There is no general support for rigid body dynamics in GROMACS. >>> >>> Mark >>> >>>> On Tue, May 8, 2018, 12:52 Qasim Pars <[email protected]> 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, >>>> -- >>>> Gromacs Users mailing list >>>> >>>> * Please search the archive at >>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>>> posting! >>>> >>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>> >>>> * For (un)subscribe requests visit >>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>>> send a mail to [email protected]. >>>> >>> -- >>> Gromacs Users mailing list >>> >>> * Please search the archive at http://www.gromacs.org/Support >>> /Mailing_Lists/GMX-Users_List before posting! >>> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >>> * For (un)subscribe requests visit >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>> send a mail to [email protected]. >>> >> >> > > -- > 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 > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to [email protected]. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected].
