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 flavours, and involve perturbing the Hamiltonian so that the ensemble it produces fits some preconceived notion, such as implementing an energy penalty for deviating from a defined value (in the case of atomic positions, dihedral angle, etc).  See the GROMACS manual for more information.

    Page last modified 05:28, 28 Dec 2010 by JLemkul?