62 citations · 279 across the 15 of their papers we have counts for
15 papers
Scalability of 3D-DFT by block tensor-matrix multiplication on the JUWELS Cluster
Nitin Malapally, Viacheslav Bolnykh, Estela Suarez +3
The 3D Discrete Fourier Transform (DFT) is a technique used to solve problems in disparate fields. Nowadays, the commonly adopted implementation of the 3D-DFT is derived from the F…
Multimap targeted free energy estimation
Andrea Rizzi, Paolo Carloni, Michele Parrinello
We present a new method to compute free energies at a quantum mechanical (QM) level of theory from molecular simulations using cheap reference potential energy functions, such as f…
Targeted free energy perturbation revisited: Accurate free energies from mapped reference potentials
Andrea Rizzi, Paolo Carloni, Michele Parrinello
We present an approach that extends the theory of targeted free energy perturbation (TFEP) to calculate free energy differences and free energy surfaces at an accurate quantum mech…
Exhaustive Search of Ligand Binding Pathways via Volume-based Metadynamics
Riccardo Capelli, Paolo Carloni, Michele Parrinello
Determining the complete set of ligands' binding/unbinding pathways is important for drug discovery and to rationally interpret mutation data. Here we have developed a metadynamics…
Open Boundary Simulations of Proteins and Their Hydration Shells by Hamiltonian Adaptive Resolution Scheme
Thomas Tarenzi, Vania Calandrini, Raffaello Potestio +2
The recently proposed Hamiltonian Adaptive Resolution Scheme (H-AdResS) allows to perform molecular simulations in an open boundary framework. It allows to change on the fly the re…
Statistical Analysis of -Holes: A Novel Complementary View on Halogen Bonding
Michal H. Kolář, Paolo Carloni, Pavel Hobza
To contribute to the understanding of noncovalent binding of halogenated molecules with a biological activity, electrostatic potential (ESP) maps of more than 2,500 compounds were…