About: NAMD goes quantum: an integrative suite for hybrid simulations

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scientific article published on 26 March 2018

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rdf:type	Item
description	wetenschappelijk artikel (nl) наукова стаття, опублікована в травні 2018 (uk) scientific article published on 26 March 2018 (en) im Mai 2018 veröffentlichter wissenschaftlicher Artikel (de) article scientifique publié en 2018 (fr) artículu científicu espublizáu en marzu de 2018 (ast)
publication date	wds:Q58009242-EB9104F8-8297-4F81-B1B7-4F57A9B2158A
publication date	2018-03-26 00:00:00Z (xsd:dateTime)
language of work or name	wds:Q58009242-2BEE21E9-125B-40B0-A3A5-92495F8BC020
language of work or name	English
exact match	wds:Q58009242-E70A8001-5C26-43EA-A1CD-F176EC85CF9B
exact match	https://scigraph.springernature.com/pub.10.1038/nmeth.4638
cites work	wds:Q58009242-0044C518-C474-4B24-B63C-755FAD539010 wds:Q58009242-0306383C-2270-4F5C-962B-E896DC33282F wds:Q58009242-0477DE32-E9EA-4058-8AC7-75C09A3BC534 wds:Q58009242-0A6499E5-F265-40A6-8BEA-E6842F69A924 wds:Q58009242-118A03F0-8903-4937-BA36-967E40A1E2DF wds:Q58009242-1B1F531A-1BCC-4DB4-8A77-1D93C8299A5C wds:Q58009242-1D6084F6-A9D1-4CAB-86F7-3EDB07092D15 wds:Q58009242-1ED53797-C694-4697-B2AF-52877FD99C05 wds:Q58009242-23351FC3-3D42-490B-BAF1-83BB4B27E47A wds:Q58009242-2D303E1E-F0F5-4DD4-9EFC-FE6ABF6623DC wds:Q58009242-2FC6A600-F265-434D-9855-254D61BE41D5 wds:Q58009242-3042771B-4728-4FD1-8F21-3D14ACB913DF wds:Q58009242-34E00ECC-8B7B-4313-ABE8-6E4884F0D53D wds:Q58009242-4786ADFD-DEE2-40EC-87F6-1380EBB2485F wds:Q58009242-4D4BB2E2-AFD0-4135-9C13-6645BBFD90D9 wds:Q58009242-4E0212FF-7DDF-46D9-901E-6C13A1E27EEA wds:Q58009242-510E3225-F7CB-4C14-809F-FA0235DBDAC3 wds:Q58009242-524E003D-1629-4729-BA40-F1DAC7BF569B wds:Q58009242-566ED035-C4E4-4312-A057-88E214357276 wds:Q58009242-65A01979-41B9-4A51-86AD-536E9EB1548D wds:Q58009242-6BE78B3C-70B5-4103-8190-73D2BDA9EAB2 wds:Q58009242-6CADDA94-ED4F-4C26-B7A7-4D9A7471F860 wds:Q58009242-984485EC-C794-4D27-8159-445EC289F0C2 wds:Q58009242-9F4AC0D8-95FE-4FDC-825A-72CB0B9BFAAC wds:Q58009242-A0E3F6CE-6E8C-42D0-BAA4-270ADC1C852B wds:Q58009242-A57A0ABF-CD8B-44A2-AF98-1A58499C9DA2 wds:Q58009242-A720CFB4-4523-4135-984A-68CA3BAE6698 wds:Q58009242-A88C365E-376D-4CD7-994B-5EE4E1AF4196 wds:Q58009242-B7AEDDD0-4FB3-47A3-B243-63C791EF65CB wds:Q58009242-BB0C5156-30CF-4341-8BE4-38C8A0AA6CCF wds:Q58009242-BC4CED2B-FB47-4524-9E44-3DC6C811E0F4 wds:Q58009242-D2239E38-4E0A-48DB-A534-7A867A89B1F0 wds:Q58009242-D2CE79AE-571E-48C5-96C6-1A77B0A70E3C wds:Q58009242-E70D6A05-A4AF-4DE7-B556-CC523CFE1EB0 wds:Q58009242-ECCC95EA-AB95-40A0-94C0-5691A6C304F6 wds:Q58009242-F08F7EDE-F875-46A4-BFC1-05504EEF963F wds:Q58009242-FA90B5C7-5FD9-4F29-84DE-2718E4EF474F wds:Q58009242-FEFAC6A5-AA9E-476A-A10B-57AB21EFDA44
cites work	Corrected small basis set Hartree-Fock method for large systems MOPAC: a semiempirical molecular orbital program VMD: visual molecular dynamics Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations Finding transition pathways using the string method with swarms of trajectories The implementation of a fast and accurate QM/MM potential method in Amber Importance of van der Waals Interactions in QM/MM Simulations Scalable molecular dynamics with NAMD ATP binding by glutamyl-tRNA synthetase is switched to the productive mode by tRNA binding Advances in molecular quantum chemistry contained in the Q-Chem 4 program package Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems An extensible interface for QM/MM molecular dynamics simulations with AMBER. GPU Linear Algebra Libraries and GPGPU Programming for Accelerating MOPAC Semiempirical Quantum Chemistry Calculations. Optimization of parameters for semiempirical methods VI: more modifications to the NDDO approximations and re-optimization of parameters Optimization of parameters for semiempirical methods I. Method QwikMD - Integrative Molecular Dynamics Toolkit for Novices and Experts Mapping Mechanical Force Propagation through Biomolecular Complexes Optimization of the additive CHARMM all-atom protein force field targeting improved sampling of the backbone φ, ψ and side-chain χ(1) and χ(2) dihedral angles Hybrid QM/MM Molecular Dynamics Study of Benzocaine in a Membrane Environment: How Does a Quantum Mechanical Treatment of Both Anesthetic and Lipids Affect Their Interaction. Dynamical networks in tRNA:protein complexes QM/MM methods for biomolecular systems Generalized Scalable Multiple Copy Algorithms for Molecular Dynamics Simulations in NAMD. Optimization of parameters for semiempirical methods II. Applications QM/MM: what have we learned, where are we, and where do we go from here? Computer simulation of zeolite structure and reactivity using embedded cluster methods Combined quantum mechanics/molecular mechanics (QM/MM) methods in computational enzymology Redistributed charge and dipole schemes for combined quantum mechanical and molecular mechanical calculations. Sparse maps--A systematic infrastructure for reduced-scaling electronic structure methods. II. Linear scaling domain based pair natural orbital coupled cluster theory Generating Efficient Quantum Chemistry Codes for Novel Architectures Chromophore twisting in the excited state of a photoswitchable fluorescent protein captured by time-resolved serial femtosecond crystallography. How Large Should the QM Region Be in QM/MM Calculations? The Case of Catechol O-Methyltransferase Exploring the Dependence of QM/MM Calculations of Enzyme Catalysis on the Size of the QM Region Software update: the ORCA program system, version 4.0 Exit strategies for charged tRNA from GluRS Convergence of QM/MM and Cluster Models for the Spectroscopic Properties of the Oxygen-Evolving Complex in Photosystem II. Extended Adaptive Biasing Force Algorithm. An On-the-Fly Implementation for Accurate Free-Energy Calculations. RM1 Semiempirical Quantum Chemistry: Parameters for Trivalent Lanthanum, Cerium and Praseodymium
author name string	wds:Q58009242-083A0755-9B2A-43AD-AD05-AE9C6907E8A7 wds:Q58009242-4093E1CB-0300-445F-8EF4-8F5963FCEC0F wds:Q58009242-F50502AF-54E3-45DA-BD62-C67201056EFE
author name string	Klaus Schulten John E Stone João V Ribeiro
rdfs:label	NAMD goes quantum: an integrative suite for hybrid simulations (en) NAMD goes quantum: an integrative suite for hybrid simulations (nl)
skos:prefLabel	NAMD goes quantum: an integrative suite for hybrid simulations (en) NAMD goes quantum: an integrative suite for hybrid simulations (nl)
name	NAMD goes quantum: an integrative suite for hybrid simulations (en)

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