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Harmonic restraints

The harmonic biasing method may be used to enforce fixed or moving restraints, including variants of Steered and Targeted MD. Within energy minimization runs, it allows for restrained minimization, e.g. to calculate relaxed potential energy surfaces. In the context of the colvars module, harmonic potentials are meant according to their textbook definition: $ \displaystyle V({\mbox{\boldmath {$x$}}}) = \frac{1}{2} k ({\mbox{\boldmath {$x$}}} - {\mbox{\boldmath {$x_0$}}})^2$ . Note that this differs from harmonic bond and angle potentials in common force fields, where the factor of one half is typically omitted, resulting in a non-standard definition of the force constant. A harmonic restraint is set up by a harmonic {...} block, which may contain (in addition to the standard option colvars) the following keywords:

Tip: A complex set of restraints can be applied to a system, by defining several colvars, and applying one or more harmonic restraints to different groups of colvars. In some cases, dozens of colvars can be defined, but their value may not be relevant: to limit the size of the colvars trajectory file, it may be wise to disable outputValue for such ``ancillary'' variables, and leave it enabled only for ``relevant'' ones.

Moving restraints: steered molecular dynamics

The following options allow to change gradually the centers of the harmonic restraints during a simulations. When the centers are changed continuously, a steered MD in a collective variable space is carried out.

Note on restarting moving restraint simulations: Information about the current step and stage of a simulation with moving restraints is stored in the restart file (state file). Thus, such simulations can be run in several chunks, and restarted directly using the same colvars configuration file. In case of a restart, the values of parameters such as targetCenters, targetNumSteps, etc. should not be changed manually.

Moving restraints: umbrella sampling

The centers of the harmonic restraints can also be changed in discrete stages: in this cases a one-dimensional umbrella sampling simulation is performed. The sampling windows in simulation are calculated in sequence. The colvars trajectory file may then be used both to evaluate the correlation times between consecutive windows, and to calculate the frequency distribution of the colvar of interest in each window. Furthermore, frequency distributions on a predefined grid can be automatically obtained by using the histogram bias (see 13.5.6).

To activate an umbrella sampling simulation, the same keywords as in the previous section can be used, with the addition of the following:

Changing force constant

The force constant of the harmonic restraint may also be changed to equilibrate [51].

next up previous contents index
Next: Linear restraints Up: Biasing and analysis methods Previous: Metadynamics   Contents   Index