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

Justin A. Lemkul jalemkul at vt.edu
Tue Jan 5 22:11:34 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? 

This is all specified in the [bonds] directive in the .top file.  See Chapter 5 
of the manual.


> Thanks in advance 
> University of Westminster
> London UK


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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