Zobrazeno 1 - 10
of 80
pro vyhledávání: '"Andrew C Simmonett"'
Autor:
Peter Eastman, Jason Swails, John D Chodera, Robert T McGibbon, Yutong Zhao, Kyle A Beauchamp, Lee-Ping Wang, Andrew C Simmonett, Matthew P Harrigan, Chaya D Stern, Rafal P Wiewiora, Bernard R Brooks, Vijay S Pande
Publikováno v:
PLoS Computational Biology, Vol 13, Iss 7, p e1005659 (2017)
OpenMM is a molecular dynamics simulation toolkit with a unique focus on extensibility. It allows users to easily add new features, including forces with novel functional forms, new integration algorithms, and new simulation protocols. Those features
Externí odkaz:
https://doaj.org/article/a3c536fb0ab14c8bbc0cb33e5bac84f0
Autor:
Marc Riera, Christopher Knight, Ethan F. Bull-Vulpe, Xuanyu Zhu, Daniel G.A. Smith, Andrew C. Simmonett, Francesco Paesani
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 representations of many-body in
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::67cb5f1b55cd7e8b265a1b10e921cdeb
https://doi.org/10.26434/chemrxiv-2023-09jh3
https://doi.org/10.26434/chemrxiv-2023-09jh3
Autor:
Johannes Steinmetzer, Daniel A. Smith, C. David Sherrill, Mark S. Gordon, Nuwan De Silva, Jamshed Anwar, Fang Liu, Henry F. Schaefer, Justin M. Turney, Lee-Ping Wang, Maximilian Scheurer, Annabelle Lolinco, Doaa Altarawy, Jiří Šponer, John D. Chodera, Carlos H. Borca, Rollin A. King, Asem Alenaizan, Jeffrey B. Schriber, David Dotson, Jonathon P. Misiewicz, Heather J. Kulik, Andrew C. Simmonett, Jeffrey R. Wagner, Sebastian J. R. Lee, Theresa L. Windus, Taylor A. Barnes, Peter Kraus, Matthew Welborn, Lori A. Burns, Logan Ward, Andreas Dreuw, Holger Kruse, Devin A. Matthews, Jiyoung Lee, Farhad Ramezanghorbani, Jan Hermann, Roberto Di Remigio, Levi N. Naden, Todd J. Martínez, Joshua T. Horton, John F. Stanton, Sebastian Ehlert, Colton B. Hicks, Adrian G. Hurtado, Zachary L. Glick, Alexander G. Heide, Michael F. Herbst
Publikováno v:
The Journal of chemical physics, vol 155, iss 20
J Chem Phys
J Chem Phys
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 be achieved with a sing
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::48b3b4d904ba13577747299327cdf641
https://resolver.caltech.edu/CaltechAUTHORS:20211206-452781343
https://resolver.caltech.edu/CaltechAUTHORS:20211206-452781343
Autor:
Richard W. Pastor, Dirk Reith, Andreas Krämer, Jing Huang, Bernard R. Brooks, Frank C. Pickard, Richard M. Venable, Andrew C. Simmonett, Karl N. Kirschner
Publikováno v:
Journal of Chemical Theory and Computation. 15:3854-3867
Atomistic biomolecular simulations predominantly utilize additive force fields (FF), where the electrostatic potential is modeled by fixed point charges. Among other consequences, the lack of polarizability in these models undermines the balance of h
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::8a58f0f0ef1ff93bedbec818b76bf8ab
https://doi.org/10.1021/acs.jctc.9b00016
https://doi.org/10.1021/acs.jctc.9b00016
Autor:
Bernard R. Brooks, Andrew C. Simmonett
Publikováno v:
J Chem Phys
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 [Formula: see text] complexity. Despite this widespread use, spanning more than t
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::a6d27666ee5125554f9c49d64846bcaa
https://europepmc.org/articles/PMC8064412/
https://europepmc.org/articles/PMC8064412/
Autor:
Richard W. Pastor, Yalun Yu, Andreas Krämer, Bernard R. Brooks, Jeffery B. Klauda, Alexander D. MacKerell, Andrew C. Simmonett, Richard M. Venable
Publikováno v:
J Chem Theory Comput
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 quantum mechanical data and free energy calculations of model c
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::d018a581185c8ead412d3cccce759ce4
https://europepmc.org/articles/PMC8059446/
https://europepmc.org/articles/PMC8059446/
Publikováno v:
Journal of computational chemistryREFERENCES. 42(19)
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 the P1 space group is supported for period
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::3cbe0a846a5e39ea48a0d882516713ad
https://pubmed.ncbi.nlm.nih.gov/33977553
https://pubmed.ncbi.nlm.nih.gov/33977553
Autor:
Andrew C. Simmonett, Nanjie Deng, Daniel R. Roe, Lieyang Chen, Anthony Cruz, Tom Kurtzman, Lauren Wickstrom
Publikováno v:
J Chem Theory Comput
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 non-bonded i
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::93b66ed65f60e29117f95f6a92944ccc
https://doi.org/10.26434/chemrxiv.13140011.v1
https://doi.org/10.26434/chemrxiv.13140011.v1
Autor:
Bernard R. Brooks, Robert A. Shaw, Uğur Bozkaya, Holger Kruse, C. David Sherrill, Francesco A. Evangelista, Konrad Patkowski, Susi Lehtola, A. Eugene DePrince, Zachary L. Glick, Maximilian Scheurer, Lori A. Burns, Matthew C. Schieber, T. Daniel Crawford, Peter Kraus, Justin M. Turney, Rollin A. King, Jonathon P. Misiewicz, Dominic A. Sirianni, Ashutosh Kumar, Yi Xie, Alexander Yu. Sokolov, Jonathan M. Waldrop, Jeffrey B. Schriber, Edward G. Hohenstein, Andrew C. Simmonett, Daniel G. A. Smith, Robert M. Parrish, Joseph Senan O’Brien, Henry F. Schaefer, Raimondas Galvelis, Roberto Di Remigio, Asem Alenaizan, Andrew M. James, Benjamin P. Pritchard
Publikováno v:
J Chem Phys
Psi4 is a free and open-source ab initio electronic structure program providing Hartree–Fock, density functional theory, many-body perturbation theory, configuration interaction, density cumulant theory, symmetry-adapted perturbation theory, and co
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::22e4072a26698e2bfbeb8fcbfc3247b2
https://europepmc.org/articles/PMC7228781/
https://europepmc.org/articles/PMC7228781/
Publikováno v:
Biophysical Journal. 120:175a-176a
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::47494a36e20422f07be42fc7107e1b0e
https://doi.org/10.1016/j.bpj.2020.11.1233
https://doi.org/10.1016/j.bpj.2020.11.1233