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Position RestraintsThe position restraint algorithm is used to restrain particles/atoms at a fixed reference position. Thus, an atom can move, but there is a large energy penalty for doing so. Reasons for using position restraints:
Position restraint sections can be added to the topology file and activated when required using the include file mechanism. If you use pdb2gmx, the Position restraint sections must be physically located in the [ moleculetype ] that is to be restrained. You cannot have a global position restraints section in your .top file. See the related error information. Special position restraint .itp files can be created using the genrestr utility (genpr in GROMACS version 3.3.x and earlier). For example, if you wish to apply position restraints to only the backbone atoms of your protein, use genrestr and choose "Backbone" as the output group, and ExamplePosition restraints requires the following information, which is placed within the topology file (.top or .itp):
[ moleculetype] This_one [ position_restraints ] ; ai funct fcx fcy fcz 1 1 1000 1000 1000 ; restrains to a point 2 1 1000 0 1000 ; restrains to a line (y-axis) 2 1 1000 0 0 ; restrains to a plane (y-z-plane) [ moleculetype ] That_one ... [ position_restraints ] ; ai funct fcx fcy fcz 1 1 1000 1000 1000 ; restrains to a point 2 1 1000 0 1000 ; restrains to a line (y-axis) 2 1 1000 0 0 ; restrains to a plane (y-z-plane) ; Note that the atom indices ai are relative to the [moleculetype], not the whole coordinate file Resources
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