2 results match your criteria: "Université Paris 13[Affiliation]"
Molecular Dynamics Simulations Enforcing Nonperiodic Boundary Conditions: New Developments and Application to the Solvent Shifts of Nitroxide Magnetic Parameters.
J Chem Theory Comput
April 2022
Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy.
Multiscale methods combining quantum mechanics and molecular mechanics (QM/MM) have become the most suitable and effective strategies for the investigation of the spectroscopic properties of medium-to-large size chromophores in condensed phases. In this context, we are developing a novel workflow aimed at improving the generality, reliability, and ease of use of the available computational tools. In this paper, we report our latest developments with specific reference to a general protocol based on atomistic simulations, carried out under nonperiodic boundary conditions (NPBC).
View Article and Find Full Text PDFRefining Collective Coordinates and Improving Free Energy Representation in Variational Enhanced Sampling.
J Chem Theory Comput
June 2018
Department of Chemistry and Applied Biosciences , ETH Zurich , c/o USI Campus, Via Giuseppe Buffi 13 , Lugano , Ticino CH-6900 , Switzerland.
Article Synopsis
- Collective variables are essential for enhanced sampling methods but finding effective ones can be difficult.
- A recent study combined techniques to improve these variables from lower quality options, specifically in the context of metadynamics.
- The new method was applied to alanine-3 in water, successfully extracting more accurate collective variables that detail the protein complex's free energy surface.