The multiple state transition path sampling method allows sampling of rare transitions between many metastable states, but has the drawback that switching between qualitatively different pathways is difficult. Combination with replica exchange transition interface sampling can in principle alleviate this problem, but requires a large number of simultaneous replicas. Here we remove these drawbacks by introducing a single replica sampling algorithm that samples only one interface at a time, while efficiently walking through the entire path space using a Wang-Landau approach or, alternatively, a fixed bias. We illustrate the method on several model systems: a particle diffusing in a simple 2D potential, isomerization in a small Lennard Jones c...
BACKGROUND For biomacromolecules or their assemblies, experimental knowledge is often restricted to...
Transition path sampling techniques allow molecular dynamics simulations of complex systems to focus...
We address the problem of sampling double-ended diffusive paths. The ensemble of paths is expressed ...
The multiple state transition interface sampling (TIS) framework in principle allows the simulation ...
In the past 15 years transition path sampling (TPS) has evolved from its basic algorithm to an entir...
Transition path sampling (TPS) was developed for studying activated processes in complex systems wit...
Nearly 20 years ago, transition path sampling (TPS) emerged as an alternative method to free energy ...
We developed a multiple state transition path sampling (TPS) approach in which it is possible to sim...
Interest in atomically detailed simulations has grown significantly with recent advances in computat...
We briefly review simulation schemes for the investigation of rare transitions and resume the recent...
Path sampling approaches have become invaluable tools to explore the mechanisms and dynamics of so-c...
We derive a novel efficient scheme to measure the rate constant of transitions between stable states...
ABSTRACT: The computational study of conformational transitions in RNA and proteins with atomistic m...
We review two recently developed efficient methods for calculating rate constants of processes domin...
We have applied the recently developed multiple state transition interface sampling approach to alan...
BACKGROUND For biomacromolecules or their assemblies, experimental knowledge is often restricted to...
Transition path sampling techniques allow molecular dynamics simulations of complex systems to focus...
We address the problem of sampling double-ended diffusive paths. The ensemble of paths is expressed ...
The multiple state transition interface sampling (TIS) framework in principle allows the simulation ...
In the past 15 years transition path sampling (TPS) has evolved from its basic algorithm to an entir...
Transition path sampling (TPS) was developed for studying activated processes in complex systems wit...
Nearly 20 years ago, transition path sampling (TPS) emerged as an alternative method to free energy ...
We developed a multiple state transition path sampling (TPS) approach in which it is possible to sim...
Interest in atomically detailed simulations has grown significantly with recent advances in computat...
We briefly review simulation schemes for the investigation of rare transitions and resume the recent...
Path sampling approaches have become invaluable tools to explore the mechanisms and dynamics of so-c...
We derive a novel efficient scheme to measure the rate constant of transitions between stable states...
ABSTRACT: The computational study of conformational transitions in RNA and proteins with atomistic m...
We review two recently developed efficient methods for calculating rate constants of processes domin...
We have applied the recently developed multiple state transition interface sampling approach to alan...
BACKGROUND For biomacromolecules or their assemblies, experimental knowledge is often restricted to...
Transition path sampling techniques allow molecular dynamics simulations of complex systems to focus...
We address the problem of sampling double-ended diffusive paths. The ensemble of paths is expressed ...