Gromacs

Constraints and Restraints

    Table of contents
    1. 1. Types of Constraints
    2. 2. References

    In GROMACS, "constraints" and "restraints" refer to different simulation processes. Constraints are used to fix the length of bonds or angles (or a subset thereof) after the integration of forces. Restraints come in a number of flavors, and involve perturbing the Hamiltonian such that the ensemble it produces fits some preconceived notion.  Restraints are typically implemented by applying an energy penalty for deviating from a defined value (in the case of atomic positions, intramolecular distances, and dihedral angles). Freeze groups can have similar applications. See the GROMACS manual for more information on all of these.

     

    Types of Constraints

    There are two main constraint algorithms implemented in GROMACS - LINCS/P-LINCS and SHAKE.

     

    References

    Page last modified 07:05, 14 Jun 2012 by mabraham