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

Hans HEINDL hheindl at terra.es
Tue Jan 5 22:04:44 CET 2010

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

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