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- Pratyush Tiwary, Michele Parrinello
- Physical review letters
- 2013

Metadynamics is a commonly used and successful enhanced sampling method. By the introduction of a history dependent bias which depends on a restricted number of collective variables it can explore complex free energy surfaces characterized by several metastable states separated by large free energy barriers. Here we extend its scope by introducing a simple… (More)

- Matteo Salvalaglio, Pratyush Tiwary, Michele Parrinello
- Journal of chemical theory and computation
- 2014

Sampling a molecular process characterized by an activation free energy significantly larger than kBT is a well-known challenge in molecular dynamics simulations. In a recent work [Tiwary and Parrinello, Phys. Rev. Lett. 2013, 111, 230602], we have demonstrated that the transition times of activated molecular transformations can be computed from… (More)

- Pratyush Tiwary, Michele Parrinello
- The journal of physical chemistry. B
- 2015

Metadynamics is a powerful and well-established enhanced sampling method for exploring and quantifying free energy surfaces of complex systems as a function of appropriately chosen variables. In the limit of long simulation time, metadynamics converges to the exact free energy surface plus a time-dependent constant. In this article, we analyze in detail… (More)

- Pratyush Tiwary, Vittorio Limongelli, Matteo Salvalaglio, Michele Parrinello
- Proceedings of the National Academy of Sciences…
- 2015

The ability to predict the mechanisms and the associated rate constants of protein-ligand unbinding is of great practical importance in drug design. In this work we demonstrate how a recently introduced metadynamics-based approach allows exploration of the unbinding pathways, estimation of the rates, and determination of the rate-limiting steps in the… (More)

- Omar Valsson, Pratyush Tiwary, Michele Parrinello
- Annual review of physical chemistry
- 2016

Atomistic simulations play a central role in many fields of science. However, their usefulness is often limited by the fact that many systems are characterized by several metastable states separated by high barriers, leading to kinetic bottlenecks. Transitions between metastable states are thus rare events that occur on significantly longer timescales than… (More)

- Pratyush Tiwary, Jagannath Mondal, Joseph A Morrone, Bruce J. Berne
- Proceedings of the National Academy of Sciences…
- 2015

A key factor influencing a drug's efficacy is its residence time in the binding pocket of the host protein. Using atomistic computer simulation to predict this residence time and the associated dissociation process is a desirable but extremely difficult task due to the long timescales involved. This gets further complicated by the presence of biophysical… (More)

- James J McCarty, Omar Valsson, Pratyush Tiwary, Michele Parrinello
- Physical review letters
- 2015

We propose a new method to obtain kinetic properties of infrequent events from molecular dynamics simulation. The procedure employs a recently introduced variational approach [Valsson and Parrinello, Phys. Rev. Lett. 113, 090601 (2014)] to construct a bias potential as a function of several collective variables that is designed to flood the associated free… (More)

- Pratyush Tiwary, Bruce J. Berne
- Proceedings of the National Academy of Sciences…
- 2016

In modern-day simulations of many-body systems, much of the computational complexity is shifted to the identification of slowly changing molecular order parameters called collective variables (CVs) or reaction coordinates. A vast array of enhanced-sampling methods are based on the identification and biasing of these low-dimensional order parameters, whose… (More)

We propose a hybrid deterministic and stochastic approach to achieve extended time scales in atomistic simulations that combines the strengths of molecular dynamics (MD) and Monte Carlo (MC) simulations in an easy-to-implement way. The method exploits the rare event nature of the dynamics similar to most current accelerated MD approaches but goes beyond… (More)

- A. van de Walle, Pratyush Tiwary, +7 authors Z. Q. Liu
- 2013

We present a new algorithm to generate Special Quasirandom Structures (SQS), i.e., best periodic supercell approximations to the true disordered state for a given number of atoms per supercell. The method is based on a Monte Carlo simulated annealing loop with an objective function that seeks to perfectly match the maximum number of correlation functions… (More)