205 related articles for article (PubMed ID: 32479082)
1. Computational Modeling of Ion Transport in Bulk and through a Nanopore Using the Drude Polarizable Force Field.
Prajapati JD; Mele C; Aksoyoglu MA; Winterhalter M; Kleinekathöfer U
J Chem Inf Model; 2020 Jun; 60(6):3188-3203. PubMed ID: 32479082
[TBL] [Abstract][Full Text] [Related]
2. Further Optimization and Validation of the Classical Drude Polarizable Protein Force Field.
Lin FY; Huang J; Pandey P; Rupakheti C; Li J; Roux BT; MacKerell AD
J Chem Theory Comput; 2020 May; 16(5):3221-3239. PubMed ID: 32282198
[TBL] [Abstract][Full Text] [Related]
3. Improved Modeling of Halogenated Ligand-Protein Interactions Using the Drude Polarizable and CHARMM Additive Empirical Force Fields.
Lin FY; MacKerell AD
J Chem Inf Model; 2019 Jan; 59(1):215-228. PubMed ID: 30418023
[TBL] [Abstract][Full Text] [Related]
4. Prediction of the concentration dependence of the surface tension and density of salt solutions: atomistic simulations using Drude oscillator polarizable and nonpolarizable models.
Neyt JC; Wender A; Lachet V; Ghoufi A; Malfreyt P
Phys Chem Chem Phys; 2013 Jul; 15(28):11679-90. PubMed ID: 23752676
[TBL] [Abstract][Full Text] [Related]
5. CHARMM-GUI Drude prepper for molecular dynamics simulation using the classical Drude polarizable force field.
Kognole AA; Lee J; Park SJ; Jo S; Chatterjee P; Lemkul JA; Huang J; MacKerell AD; Im W
J Comput Chem; 2022 Feb; 43(5):359-375. PubMed ID: 34874077
[TBL] [Abstract][Full Text] [Related]
6. Polarizable Force Field for Molecular Ions Based on the Classical Drude Oscillator.
Lin FY; Lopes PEM; Harder E; Roux B; MacKerell AD
J Chem Inf Model; 2018 May; 58(5):993-1004. PubMed ID: 29624370
[TBL] [Abstract][Full Text] [Related]
7. Accurate modeling of RNA hairpins through the explicit treatment of electronic polarizability with the classical Drude oscillator force field.
Sengul MY; MacKerell AD
J Comput Biophys Chem; 2022 Jun; 21(4):461-471. PubMed ID: 35756549
[TBL] [Abstract][Full Text] [Related]
8. Electrostatic properties of aqueous salt solution interfaces: a comparison of polarizable and nonpolarizable ion models.
Warren GL; Patel S
J Phys Chem B; 2008 Sep; 112(37):11679-93. PubMed ID: 18712908
[TBL] [Abstract][Full Text] [Related]
9. Benchmarking polarizable and non-polarizable force fields for Ca
Amin KS; Hu X; Salahub DR; Baldauf C; Lim C; Noskov S
J Chem Phys; 2020 Oct; 153(14):144102. PubMed ID: 33086838
[TBL] [Abstract][Full Text] [Related]
10. Balancing the interactions of ions, water, and DNA in the Drude polarizable force field.
Savelyev A; MacKerell AD
J Phys Chem B; 2014 Jun; 118(24):6742-57. PubMed ID: 24874104
[TBL] [Abstract][Full Text] [Related]
11. High-performance scalable molecular dynamics simulations of a polarizable force field based on classical Drude oscillators in NAMD.
Jiang W; Hardy DJ; Phillips JC; Mackerell AD; Schulten K; Roux B
J Phys Chem Lett; 2011; 2(2):87-92. PubMed ID: 21572567
[TBL] [Abstract][Full Text] [Related]
12. Polarizable Molecular Dynamics Simulations of Two
Salsbury AM; Dean TJ; Lemkul JA
J Chem Theory Comput; 2020 May; 16(5):3430-3444. PubMed ID: 32307997
[TBL] [Abstract][Full Text] [Related]
13. Competition among Li(+), Na(+), K(+), and Rb(+) monovalent ions for DNA in molecular dynamics simulations using the additive CHARMM36 and Drude polarizable force fields.
Savelyev A; MacKerell AD
J Phys Chem B; 2015 Mar; 119(12):4428-40. PubMed ID: 25751286
[TBL] [Abstract][Full Text] [Related]
14. p
Aleksandrov A; Roux B; MacKerell AD
J Chem Theory Comput; 2020 Jul; 16(7):4655-4668. PubMed ID: 32464053
[TBL] [Abstract][Full Text] [Related]
15. Improved Modeling of Cation-π and Anion-Ring Interactions Using the Drude Polarizable Empirical Force Field for Proteins.
Lin FY; MacKerell AD
J Comput Chem; 2020 Feb; 41(5):439-448. PubMed ID: 31518010
[TBL] [Abstract][Full Text] [Related]
16. Molecular Modeling of Water-in-Salt Electrolytes: A Comprehensive Analysis of Polarization Effects and Force Field Parameters in Molecular Dynamics Simulations.
Rezaei M; Sakong S; Groß A
J Chem Theory Comput; 2023 Sep; 19(17):5712-5730. PubMed ID: 37528639
[TBL] [Abstract][Full Text] [Related]
17. A theoretical study of aqueous solvation of K comparing ab initio, polarizable, and fixed-charge models.
Whitfield TW; Varma S; Harder E; Lamoureux G; Rempe SB; Roux B
J Chem Theory Comput; 2007; 3(6):2068-2082. PubMed ID: 21785577
[TBL] [Abstract][Full Text] [Related]
18. Drude Polarizable Lipid Force Field with Explicit Treatment of Long-Range Dispersion: Parametrization and Validation for Saturated and Monounsaturated Zwitterionic Lipids.
Yu Y; Venable RM; Thirman J; Chatterjee P; Kumar A; Pastor RW; Roux B; MacKerell AD; Klauda JB
J Chem Theory Comput; 2023 May; 19(9):2590-2605. PubMed ID: 37071552
[TBL] [Abstract][Full Text] [Related]
19. Benchmarking the Drude Polarizable Force Field Using the r(GACC) Tetranucleotide.
Winkler L; Cheatham TE
J Chem Inf Model; 2023 Apr; 63(8):2505-2511. PubMed ID: 36996447
[TBL] [Abstract][Full Text] [Related]
20. Development of CHARMM polarizable force field for nucleic acid bases based on the classical Drude oscillator model.
Baker CM; Anisimov VM; MacKerell AD
J Phys Chem B; 2011 Jan; 115(3):580-96. PubMed ID: 21166469
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]
