DISCOTRESS

DISCOTRESS is a C++ program to simulate and analyze the dynamics on kinetic transition networks, beyond the functionality provided in PATHSAMPLE. DISCOTRESS is written and maintained by Daniel J. Sharpe, and can be found here.

Functionality

DISCOTRESS contains implementations of state-of-the-art algorithms to robustly and efficiently perform quantitative analyses of a kinetic network. Some recommended functionality that is very powerful for gaining a detailed understanding of your kinetic network is as follows:

• simulate trajectories by kinetic path sampling, thereby sampling the first passage time distribution and obtaining a numerical estimate for the time-dependent occupation probability distribution of macrostates

• calculate the probability of visiting states on a direct transition path between two endpoint states

• calculate the committor probabilities for all nodes of the network (and hence analyze the network by equilibrium or nonequilibrium transition path theory)

• decompose the ensemble of first passage paths into a finite set of flux-paths and their associated contributions to the net productive flux

Getting Started

DISCOTRESS has its own system of input files, so first you will need to convert your kinetic network database from PATHSAMPLE format (min.data, ts.data). You will need to construct the following 3 files:

• edge_conns.dat - two-column file containing a list of connections, can be extracted straightforwardly as the corresponding columns of ts.data

• edge_weights.dat - two-column file containing the natural log of transition rates corresponding to the entries in edge_conns.dat. You will need to dump these data from PATHSAMPLE (Fortran script available)

• stat_prob.dat - single-column file containing the natural log of stationary probabilities of nodes in the network. You will need to dump these data, which are directly related to the energies of minima, from PATHSAMPLE (Fortran script available).

Further information on these DISCOTRESS input files and others, including the input.kmc file of keywords, is available here.

Further helpful scripts to analyze the output of DISCOTRESS are available here.

Analyzing your database

The routines that are implemented in DISCOTRESS allow for numerous detailed analyses of kinetic networks that are not possible by conventional methods. You may wish to conduct a particular analysis to complement your initial report of the database and validate your qualitative observations based on the topology of the energy landscape. Alternatively, you may wish to conduct an extensive quantitative analysis of a database that you have constructed in a separate report. Using DISCOTRESS, you can e.g. find the key transition paths that facilitate the productive transition between endpoint states (by shortest paths analysis, transition path theory, or simulation of trajectories) and identify the key states that mediate these pathways (by calculating reactive visitation probabilities, committor probabilities, etc.)

A presentation ("Sharpe - Recent advances in the numerical analysis of finite Markov chains") describing the quantitative methods is available in the "AVT presentations" folder of the Wales group google drive here.

Tutorials

Tutorials are available here.

FAQs

Answers to some FAQs are available here.