[gmx-users] define a new covalent bond in gromacs
hheindl at terra.es
Tue Jan 5 22:15:23 CET 2010
mdrun-openmm does not yet support any restraints
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
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