Fragmentation methods: A route to accurate calculations on large systems

MS Gordon, DG Fedorov, SR Pruitt… - Chemical …, 2012 - ACS Publications
Theoretical chemists have always strived to perform quantum mechanics (QM) calculations
on larger and larger molecules and molecular systems, as well as condensed phase …

Large-scale computations in chemistry: a bird's eye view of a vibrant field

AV Akimov, OV Prezhdo - Chemical reviews, 2015 - ACS Publications
1.1. The Meaning of “Large Scale” In general, the term “large scale” can have one of the
following five meanings in computational chemistry:(1) large size: power-law and …

Exploring chemistry with the fragment molecular orbital method

DG Fedorov, T Nagata, K Kitaura - Physical Chemistry Chemical …, 2012 - pubs.rsc.org
The fragment molecular orbital (FMO) method makes possible nearly linear scaling
calculations of large molecular systems, such as water clusters, proteins and DNA. In …

DeepQMC: An open-source software suite for variational optimization of deep-learning molecular wave functions

Z Schätzle, PB Szabó, M Mezera… - The Journal of …, 2023 - pubs.aip.org
Computing accurate yet efficient approximations to the solutions of the electronic
Schrödinger equation has been a paramount challenge of computational chemistry for …

The fragment molecular orbital method: theoretical development, implementation in GAMESS, and applications

DG Fedorov - Wiley Interdisciplinary Reviews: Computational …, 2017 - Wiley Online Library
The physical picture of the fragment molecular orbital (FMO) method is described on the
basis of a many‐body expansion with terms describing the polarization of isolated …

Recent advances in quantum fragmentation approaches to complex molecular and condensed‐phase systems

J Liu, X He - Wiley Interdisciplinary Reviews: Computational …, 2023 - Wiley Online Library
Quantum mechanical (QM) calculations are critical in quantitatively understanding the
relationship between the structure and physicochemical properties of various chemical …

Fragment quantum mechanical calculation of proteins and its applications

X He, T Zhu, X Wang, J Liu… - Accounts of chemical …, 2014 - ACS Publications
Conspectus The desire to study molecular systems that are much larger than what the
current state-of-the-art ab initio or density functional theory methods could handle has …

Molecules-in-molecules: An extrapolated fragment-based approach for accurate calculations on large molecules and materials

NJ Mayhall, K Raghavachari - Journal of chemical theory and …, 2011 - ACS Publications
We present a new extrapolated fragment-based approach, termed molecules-in-molecules
(MIM), for accurate energy calculations on large molecules. In this method, we use a …

Linear scaling self-consistent field calculations with millions of atoms in the condensed phase

J VandeVondele, U Borstnik… - Journal of chemical theory …, 2012 - ACS Publications
In this work, the applicability and performance of a linear scaling algorithm is investigated for
three-dimensional condensed phase systems. A simple but robust approach based on the …

[HTML][HTML] The BioFragment Database (BFDb): An open-data platform for computational chemistry analysis of noncovalent interactions

LA Burns, JC Faver, Z Zheng, MS Marshall… - The Journal of …, 2017 - pubs.aip.org
Accurate potential energy models are necessary for reliable atomistic simulations of
chemical phenomena. In the realm of biomolecular modeling, large systems like proteins …