Constraints and Restraints

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    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).  See the GROMACS manual for more information.



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