Gromacs

Position Restraints

    Table of contents
    1. 1. Example
    2. 2. Resources

    The 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:

    • avoiding drastic rearrangement of critical parts of the system, e.g. restrain the protein during equilibration of added solvent.
    • isolation of a region being studied in detail, using a restrained shell of particles, from region outside it which lacks proper interactions due to missing particles (not implemented in GROMACS).

    Position restraint sections can be added to the topology file and activated when required using the include file mechanism. If you use pdb2gmx, the -i option makes it write a posre.itp file for your non-hydrogen atoms. This is then included in the topology file. You control whether or not the above lines are actually read by setting define = -DPOSRES option in the .mdp file.

    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 #include "backbone_posre.itp" in your topology.

    Example

    Position restraints requires the following information, which is placed within the topology file (.top or .itp):

    • identification of the atom / particle it is to be applied to (within the [moleculetype] not the coordinate file),
    • the function type,
    • the force constant in each dimension (x, y, z).
    [ 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

    • See GROMACS Manual, Section 4.3.1 for details on the equations used to implement position restraints within the GROMACS.
    • See GROMACS Manual, Section 5.6.1 for details on how positions restraints are implemented within a molecule topology file.
    Page last modified 11:12, 26 Jul 2012 by mabraham