4 papers · 1 filter
Finding Efficient Collective Variables: The Case of Crystallization
Yue-Yu Zhang, Haiyang Niu, GiovanniMaria Piccini +2
Several enhanced sampling methods such as umbrella sampling or metadynamics rely on the identification of an appropriate set of collective variables. Recently two methods have been…
Metadynamics with Discriminants: a Tool for Understanding Chemistry
GiovanniMaria Piccini, Dan Mendels, Michele Parrinello
We introduce an extension of a recently published method\cite{Mendels2018} to obtain low-dimensional collective variables for studying multiple states free energy processes in chem…
Folding a Small Protein Using Harmonic Linear Discriminant Analysis
Dan Mendels, Giovannimaria Piccini, Z. Faidon Brotzakis +2
Many processes of scientific importance are characterized by time scales that extend far beyond the reach of standard simulation techniques. To circumvent this impediment a plethor…
Path collective variables without paths
Dan Mendels, GiovanniMaria Piccini, Michele Parrinello
We introduce a method to obtain one-dimensional collective variables for studying rarely occurring transitions between two metastable states separated by a high free energy barrier…