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Particle methods have become indispensible in conformation dynamics to
compute transition rates in protein folding, binding processes and
molecular design, to mention a few.
Conformation dynamics requires at a decomposition of a molecule's position
space into metastable conformations.
In this paper, we show how this decomposition
can be obtained via the design of either ``soft'' or ``hard''
molecular conformations.
We show, that the soft approach results in a larger metastabilitiy of
the decomposition and is thus more advantegous. This is illustrated
by a simulation of Alanine Dipeptide.
Markov state models (MSMs) have received an unabated increase in popularity in recent years, as they are very
well suited for the identification and analysis of metastable states and related kinetics. However, the state-of-the-art Markov state modeling methods and tools enforce the fulfillment of a
detailed balance condition, restricting their applicability to equilibrium MSMs. To date, they are unsuitable to deal with
general dominant data structures including cyclic processes, which are essentially associated with nonequilibrium systems.
To overcome this limitation, we developed a generalization of the common robust Perron Cluster Cluster Analysis (PCCA+) method, termed generalized PCCA (G-PCCA). This method handles equilibrium and nonequilibrium simulation data, utilizing Schur vectors instead of eigenvectors. G-PCCA is not limited to the detection of metastable states but enables the identification of dominant structures in a general sense, unraveling cyclic processes. This is exemplified by application of G-PCCA on nonequilibrium molecular dynamics data of the Amyloid β (1−40) peptide, periodically driven by an oscillating electric field.