242 citations · 719 across the 11 of their papers we have counts for
11 papers
Deep learning path-like collective variable for enhanced sampling molecular dynamics
Thorben Fröhlking, Luigi Bonati, Valerio Rizzi +1
Several enhanced sampling techniques rely on the definition of collective variables to effectively explore free energy landscapes. Existing variables that describe the progression…
Rare Event Kinetics from Adaptive Bias Enhanced Sampling
Dhiman Ray, Narjes Ansari, Valerio Rizzi +2
We introduce a novel enhanced sampling approach named OPES flooding for calculating the kinetics of rare events from atomistic molecular dynamics simulation. This method is derived…
Water regulates the residence time of Benzamidine in Trypsin
Narjes Ansari, Valerio Rizzi, Michele Parrinello
The process of ligand-protein unbinding is crucial in biophysics. Water is an essential part of any biological system and yet, many aspects of its role remain elusive. Here, we sim…
Collective Variables for the Study of Crystallization
Tarak Karmakar, Michele Invernizzi, Valerio Rizzi +1
The phenomenon of solidification of a substance from its liquid phase is of the greatest practical and theoretical importance, and atomistic simulations can provide precious inform…
The role of water in host-guest interaction
Valerio Rizzi, Luigi Bonati, Narjes Ansari +1
One of the main applications of atomistic computer simulations is the calculation of ligand binding energies. The accuracy of these calculations depends on the force field quality…
Data-Driven Collective Variables for Enhanced Sampling
Luigi Bonati, Valerio Rizzi, Michele Parrinello
Designing an appropriate set of collective variables is crucial to the success of several enhanced sampling methods. Here we focus on how to obtain such variables from information…