Andrew C Simmonett
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Explore the profile of Andrew C Simmonett including associated specialties, affiliations and a list of published articles.
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63
Citations
2059
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Recent Articles
1.
Hwang W, Austin S, Blondel A, Boittier E, Boresch S, Buck M, et al.
J Phys Chem B
. 2024 Sep;
128(41):9976-10042.
PMID: 39303207
Since its inception nearly a half century ago, CHARMM has been playing a central role in computational biochemistry and biophysics. Commensurate with the developments in experimental research and advances in...
2.
Nochebuena J, Simmonett A, Cisneros G
J Chem Phys
. 2024 May;
160(17).
PMID: 38747990
Hybrid quantum mechanics/molecular mechanics (QM/MM) simulations have become an essential tool in computational chemistry, particularly for analyzing complex biological and condensed phase systems. Building on this foundation, our work presents...
3.
Eastman P, Galvelis R, Pelaez R, Abreu C, Farr S, Gallicchio E, et al.
J Phys Chem B
. 2023 Dec;
128(1):109-116.
PMID: 38154096
Machine learning plays an important and growing role in molecular simulation. The newest version of the OpenMM molecular dynamics toolkit introduces new features to support the use of machine learning...
4.
Eastman P, Galvelis R, Pelaez R, Abreu C, Farr S, Gallicchio E, et al.
ArXiv
. 2023 Nov;
PMID: 37986730
Machine learning plays an important and growing role in molecular simulation. The newest version of the OpenMM molecular dynamics toolkit introduces new features to support the use of machine learning...
5.
Riera M, Knight C, Bull-Vulpe E, Zhu X, Agnew H, Smith D, et al.
J Chem Phys
. 2023 Aug;
159(5).
PMID: 37526156
Many-Body eXpansion (MBX) is a C++ library that implements many-body potential energy functions (PEFs) within the "many-body energy" (MB-nrg) formalism. MB-nrg PEFs integrate an underlying polarizable model with explicit machine-learned...
6.
Smith D, Lolinco A, Glick Z, Lee J, Alenaizan A, Barnes T, et al.
J Chem Phys
. 2021 Dec;
155(20):204801.
PMID: 34852489
Community efforts in the computational molecular sciences (CMS) are evolving toward modular, open, and interoperable interfaces that work with existing community codes to provide more functionality and composability than could...
7.
Prasad S, Simmonett A, Meana-Paneda R, Brooks B
J Comput Chem
. 2021 May;
42(19):1373-1383.
PMID: 33977553
The Eighth-Shell method for parallelization of molecular dynamics simulations has previously been shown to be the most optimal for efficiency at large process counts. However, in its current formulation only...
8.
Chen L, Cruz A, Roe D, Simmonett A, Wickstrom L, Deng N, et al.
J Chem Theory Comput
. 2021 Apr;
17(5):2714-2724.
PMID: 33830762
Grid Inhomogeneous Solvation Theory (GIST) maps out solvation thermodynamic properties on a fine meshed grid and provides a statistical mechanical formalism for thermodynamic end-state calculations. However, differences in how long-range...
9.
Simmonett A, Brooks B
J Chem Phys
. 2021 Mar;
154(10):104101.
PMID: 33722046
The particle mesh Ewald (PME) method has become ubiquitous in the molecular simulation community due to its ability to deliver long range electrostatics accurately with ONlog(N) complexity. Despite this widespread...
10.
Yu Y, Kramer A, Venable R, Simmonett A, MacKerell Jr A, Klauda J, et al.
J Chem Theory Comput
. 2021 Feb;
17(3):1562-1580.
PMID: 33620214
The development of the CHARMM lipid force field (FF) can be traced back to the early 1990s with its current version denoted CHARMM36 (C36). The parametrization of C36 utilized high-level...