533 citations · 1.9k across the 55 of their papers we have counts for
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A perturbative solution to metadynamics ordinary differential equation
Pratyush Tiwary, James F. Dama, Michele Parrinello
Metadynamics is a popular enhanced sampling scheme wherein by periodic application of a repulsive bias, one can surmount high free energy barriers and explore complex landscapes. R…
Caliber based spectral gap optimization of order parameters (SGOOP) for sampling complex molecular systems
Pratyush Tiwary, B. J. Berne
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…
Overcoming timescale and finite-size limitations to compute nucleation rates from small scale Well Tempered Metadynamics simulations
Matteo Salvalaglio, Pratyush Tiwary, Giovanni Maria Maggioni +2
Condensation of a liquid droplet from a supersaturated vapour phase is initiated by a prototypical nucleation event. As such it is challenging to compute its rate from atomistic mo…
The role of water and steric constraints in the kinetics of cavity-ligand unbinding
Pratyush Tiwary, Jagannath Mondal, Joseph A. Morrone +1
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 t…
Variationally Optimized Free Energy Flooding for Rate Calculation
James McCarty, Omar Valsson, Pratyush Tiwary +1
We propose a new method to obtain kinetic properties of infrequent events from molecular dynamics simulation. The procedure employs a recently introduced variational approach [Vals…