Sentence examples for collective variables from inspiring English sources

The sampling is accelerated by using an artificially high temperature for the collective variables.

Simulations were performed using well-tempered metadynamics combined with a path collective variables approach.

We characterize the free-energy landscape of these three fragments in terms of a few selected collective variables.

This is different from metadynamics in which there is no specific direction of the biasing force and the computational effort increases significantly with the number of collective variables.

The analysis of MD trajectories often relies on the choice of collective variables (CVs) along which the dynamics of the system is projected.

A method for sampling efficiently the free energy landscape of a complex system with respect to some given collective variables is proposed.

Emergence will come in degrees as a function of the complexity of interactions subsumed by the collective variable.

Specifically, the free energy landscape of the whole transition process was drawn by metadynamics with the path collective variable approach.

We investigate the effect of mobile ions and ion charge, as well as the choice of collective variable (CV), on the binding free energy of the peptide.

We then reconstructed the system free-energy landscape along the predetermined transition trajectories using a path collective variable approach based on metadynamics.

This was achieved by applying the Collective Variable-Driven Hyperdynamics biasing technique, which extended the inter-impact time over a range of six orders of magnitude, down to a more realistic ion-flux of 1023 m−2s−1.