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

David van der Spoel spoel at xray.bmc.uu.se
Tue Jan 5 22:12:20 CET 2010

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 
> 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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