166 related articles for article (PubMed ID: 23972860)
1. Introducing titratable water to all-atom molecular dynamics at constant pH.
Chen W; Wallace JA; Yue Z; Shen JK
Biophys J; 2013 Aug; 105(4):L15-7. PubMed ID: 23972860
[TBL] [Abstract][Full Text] [Related]
2. All-Atom Continuous Constant pH Molecular Dynamics With Particle Mesh Ewald and Titratable Water.
Huang Y; Chen W; Wallace JA; Shen J
J Chem Theory Comput; 2016 Nov; 12(11):5411-5421. PubMed ID: 27709966
[TBL] [Abstract][Full Text] [Related]
3. GPU-Accelerated Implementation of Continuous Constant pH Molecular Dynamics in Amber: p
Harris RC; Shen J
J Chem Inf Model; 2019 Nov; 59(11):4821-4832. PubMed ID: 31661616
[TBL] [Abstract][Full Text] [Related]
4. GPU-Accelerated All-Atom Particle-Mesh Ewald Continuous Constant pH Molecular Dynamics in Amber.
Harris JA; Liu R; Martins de Oliveira V; Vázquez-Montelongo EA; Henderson JA; Shen J
J Chem Theory Comput; 2022 Dec; 18(12):7510-7527. PubMed ID: 36377980
[TBL] [Abstract][Full Text] [Related]
5. On the recombination of hydronium and hydroxide ions in water.
Hassanali A; Prakash MK; Eshet H; Parrinello M
Proc Natl Acad Sci U S A; 2011 Dec; 108(51):20410-5. PubMed ID: 22143756
[TBL] [Abstract][Full Text] [Related]
6. Comparative proton transfer efficiencies of hydronium and hydroxide in aqueous solution: proton transfer vs Brownian motion.
Uddin N; Kim J; Sung BJ; Choi TH; Choi CH; Kang H
J Phys Chem B; 2014 Nov; 118(47):13671-8. PubMed ID: 25365595
[TBL] [Abstract][Full Text] [Related]
7. Continuous Constant pH Molecular Dynamics in Explicit Solvent with pH-Based Replica Exchange.
Wallace JA; Shen JK
J Chem Theory Comput; 2011 Aug; 7(8):2617-29. PubMed ID: 26606635
[TBL] [Abstract][Full Text] [Related]
8. OPEP6: A New Constant-pH Molecular Dynamics Simulation Scheme with OPEP Coarse-Grained Force Field.
Barroso da Silva FL; Sterpone F; Derreumaux P
J Chem Theory Comput; 2019 Jun; 15(6):3875-3888. PubMed ID: 31059255
[TBL] [Abstract][Full Text] [Related]
9. Proton transfer through hydrogen bonds in two-dimensional water layers: a theoretical study based on ab initio and quantum-classical simulations.
Bankura A; Chandra A
J Chem Phys; 2015 Jan; 142(4):044701. PubMed ID: 25637997
[TBL] [Abstract][Full Text] [Related]
10. Charge-leveling and proper treatment of long-range electrostatics in all-atom molecular dynamics at constant pH.
Wallace JA; Shen JK
J Chem Phys; 2012 Nov; 137(18):184105. PubMed ID: 23163362
[TBL] [Abstract][Full Text] [Related]
11. Surface affinity of the hydronium ion: the effective fragment potential and umbrella sampling.
Brorsen KR; Pruitt SR; Gordon MS
J Phys Chem B; 2014 Dec; 118(49):14382-7. PubMed ID: 25418843
[TBL] [Abstract][Full Text] [Related]
12. Generalized Born Based Continuous Constant pH Molecular Dynamics in Amber: Implementation, Benchmarking and Analysis.
Huang Y; Harris RC; Shen J
J Chem Inf Model; 2018 Jul; 58(7):1372-1383. PubMed ID: 29949356
[TBL] [Abstract][Full Text] [Related]
13. Constant pH molecular dynamics of proteins in explicit solvent with proton tautomerism.
Goh GB; Hulbert BS; Zhou H; Brooks CL
Proteins; 2014 Jul; 82(7):1319-31. PubMed ID: 24375620
[TBL] [Abstract][Full Text] [Related]
14. Proton defect solvation and dynamics in aqueous acid and base.
Kale S; Herzfeld J
Angew Chem Int Ed Engl; 2012 Oct; 51(44):11029-32. PubMed ID: 23037880
[TBL] [Abstract][Full Text] [Related]
15. Effects of system net charge and electrostatic truncation on all-atom constant pH molecular dynamics.
Chen W; Shen JK
J Comput Chem; 2014 Oct; 35(27):1986-96. PubMed ID: 25142416
[TBL] [Abstract][Full Text] [Related]
16. Constant pH Replica Exchange Molecular Dynamics in Explicit Solvent Using Discrete Protonation States: Implementation, Testing, and Validation.
Swails JM; York DM; Roitberg AE
J Chem Theory Comput; 2014 Mar; 10(3):1341-1352. PubMed ID: 24803862
[TBL] [Abstract][Full Text] [Related]
17. Charge-Neutral Constant pH Molecular Dynamics Simulations Using a Parsimonious Proton Buffer.
Donnini S; Ullmann RT; Groenhof G; Grubmüller H
J Chem Theory Comput; 2016 Mar; 12(3):1040-51. PubMed ID: 26881315
[TBL] [Abstract][Full Text] [Related]
18. Self-assembly and bilayer-micelle transition of fatty acids studied by replica-exchange constant pH molecular dynamics.
Morrow BH; Koenig PH; Shen JK
Langmuir; 2013 Dec; 29(48):14823-30. PubMed ID: 24215478
[TBL] [Abstract][Full Text] [Related]
19. Potential of mean force of water-proton bath and molecular dynamic simulation of proteins at constant pH.
Vorobjev YN
J Comput Chem; 2012 Mar; 33(8):832-42. PubMed ID: 22278814
[TBL] [Abstract][Full Text] [Related]
20. Concerted hydrogen-bond dynamics in the transport mechanism of the hydrated proton: a first-principles molecular dynamics study.
Berkelbach TC; Lee HS; Tuckerman ME
Phys Rev Lett; 2009 Dec; 103(23):238302. PubMed ID: 20366181
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]
