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physics.chem-ph2023★ 47 cited
A High-Throughput Steered Molecular Dynamics Study on the Free Energy Profile of Ion Permeation through Gramicidin A
Toni Giorgino, Gianni De Fabritiis
Steered molecular dynamics (SMD) simulations for the calculation of free energies are well suited for high-throughput molecular simulations on a distributed infrastructure due to t…
physics.chem-ph2019★ 1 cited
A Scalable Molecular Force Field Parameterization Method Based on Density Functional Theory and Quantum-Level Machine Learning
Raimondas Galvelis, Stefan Doerr, Joao M. Damas +2
Fast and accurate molecular force field (FF) parameterization is still an unsolved problem. Accurate FFs are not generally available for all molecules, like novel druglike molecule…
physics.chem-ph2013★ 1.1k cited
Identification of slow molecular order parameters for Markov model construction
Guillermo Perez-Hernandez, Fabian Paul, Toni Giorgino +2
A goal in the kinetic characterization of a macromolecular system is the description of its slow relaxation processes, involving (i) identification of the structural changes involv…