Hi, Of what would that be a good physical model?
Mark On Wed, May 9, 2018, 10:07 Ahmet Yildirim <[email protected]> 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 < > [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]. > -- 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].
