[gmx-users] define a new covalent bond in gromacs

[Hans HEINDL]

I'll try and let you know about results

Hans
Am Mittwoch, den 06.01.2010, 11:15 +0000 schrieb TJ Piggot:
> How about using bond type 6 to restrain the distance without actually 
> creating a bond between the atoms?
> 
> Tom
> 
> --On Tuesday, January 05, 2010 22:57:32 +0100 David van der Spoel 
> <spoel at xray.bmc.uu.se> wrote:
> 
> > Hans HEINDL wrote:
> >> mdrun-openmm does not yet support any restraints
> > But gromacs does. Therefore, it seems you need to patch openmm, for which
> > you probably want to contact the openmm team.
> >>
> >> Hans
> >>
> >> Am Dienstag, den 05.01.2010, 22:12 +0100 schrieb David van der Spoel:
> >>> Hans HEINDL wrote:
> >>>> Hi all,
> >>>>
> >>>> I need to restrain the distance of two atoms in my system (the distance
> >>>> is around 57 angstroms). As we plan to use mdrun-openmm which presently
> >>>> does not support neither distance nor position restraints we need to
> >>>> create a new covalent bond between the two atoms which would restrain
> >>>> the distance of the two atoms. (This was Peter Eastmans idea from
> >>>> Standford) How could we do that and where would be the best place to
> >>>> define (I presume the *.top file) the bond and where should the bond
> >>>> length and spring constant be defined?
> >>>>
> >>>> Thanks in advance
> >>>>
> >>>> Hans HEINDL
> >>>> University of Westminster
> >>>> London UK
> >>>>
> >>> How about normal distance restraints? Have you checked the manual?
> >>>
> >>> --
> >>> David van der Spoel, Ph.D., Professor of Biology
> >>> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
> >>> Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
> >>> spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
> >>
> >>
> >
> >
> > --
> > David van der Spoel, Ph.D., Professor of Biology
> > Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
> > Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
> > spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
> > --
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> 
> 
> 
> ----------------------
> TJ Piggot
> t.piggot at bristol.ac.uk
> University of Bristol, UK.
>