143 related articles for article (PubMed ID: 37093676)
1. GPU-specific algorithms for improved solute sampling in grand canonical Monte Carlo simulations.
Zhao M; Kognole AA; Jo S; Tao A; Hazel A; MacKerell AD
J Comput Chem; 2023 Jul; 44(20):1719-1732. PubMed ID: 37093676
[TBL] [Abstract][Full Text] [Related]
2. Sampling of Organic Solutes in Aqueous and Heterogeneous Environments Using Oscillating Excess Chemical Potentials in Grand Canonical-like Monte Carlo-Molecular Dynamics Simulations.
Lakkaraju SK; Raman EP; Yu W; MacKerell AD
J Chem Theory Comput; 2014 Jun; 10(6):2281-2290. PubMed ID: 24932136
[TBL] [Abstract][Full Text] [Related]
3. Enhancing sampling of water rehydration upon ligand binding using variants of grand canonical Monte Carlo.
Ge Y; Melling OJ; Dong W; Essex JW; Mobley DL
J Comput Aided Mol Des; 2022 Oct; 36(10):767-779. PubMed ID: 36198874
[TBL] [Abstract][Full Text] [Related]
4. Determination of Ionic Hydration Free Energies with Grand Canonical Monte Carlo/Molecular Dynamics Simulations in Explicit Water.
Sun D; Lakkaraju SK; Jo S; MacKerell AD
J Chem Theory Comput; 2018 Oct; 14(10):5290-5302. PubMed ID: 30183291
[TBL] [Abstract][Full Text] [Related]
5. Enhanced Grand Canonical Sampling of Occluded Water Sites Using Nonequilibrium Candidate Monte Carlo.
Melling OJ; Samways ML; Ge Y; Mobley DL; Essex JW
J Chem Theory Comput; 2023 Feb; 19(3):1050-1062. PubMed ID: 36692215
[TBL] [Abstract][Full Text] [Related]
6. Functional Group Distributions, Partition Coefficients, and Resistance Factors in Lipid Bilayers Using Site Identification by Ligand Competitive Saturation.
Lind C; Pandey P; Pastor RW; MacKerell AD
J Chem Theory Comput; 2021 May; 17(5):3188-3202. PubMed ID: 33929848
[TBL] [Abstract][Full Text] [Related]
7. py-MCMD: Python Software for Performing Hybrid Monte Carlo/Molecular Dynamics Simulations with GOMC and NAMD.
Barhaghi MS; Crawford B; Schwing G; Hardy DJ; Stone JE; Schwiebert L; Potoff J; Tajkhorshid E
J Chem Theory Comput; 2022 Aug; 18(8):4983-4994. PubMed ID: 35621307
[TBL] [Abstract][Full Text] [Related]
8. Grand canonical Monte Carlo simulations of water in protein environments.
Woo HJ; Dinner AR; Roux B
J Chem Phys; 2004 Oct; 121(13):6392-400. PubMed ID: 15446937
[TBL] [Abstract][Full Text] [Related]
9. Molecular exchange Monte Carlo: A generalized method for identity exchanges in grand canonical Monte Carlo simulations.
Soroush Barhaghi M; Torabi K; Nejahi Y; Schwiebert L; Potoff JJ
J Chem Phys; 2018 Aug; 149(7):072318. PubMed ID: 30134670
[TBL] [Abstract][Full Text] [Related]
10. Reactive Monte Carlo and grand-canonical Monte Carlo simulations of the propene metathesis reaction system.
Hansen N; Jakobtorweihen S; Keil FJ
J Chem Phys; 2005 Apr; 122(16):164705. PubMed ID: 15945697
[TBL] [Abstract][Full Text] [Related]
11. A GPU OpenCL based cross-platform Monte Carlo dose calculation engine (goMC).
Tian Z; Shi F; Folkerts M; Qin N; Jiang SB; Jia X
Phys Med Biol; 2015 Oct; 60(19):7419-35. PubMed ID: 26352012
[TBL] [Abstract][Full Text] [Related]
12. Pharmacophore modeling using site-identification by ligand competitive saturation (SILCS) with multiple probe molecules.
Yu W; Lakkaraju SK; Raman EP; Fang L; MacKerell AD
J Chem Inf Model; 2015 Feb; 55(2):407-20. PubMed ID: 25622696
[TBL] [Abstract][Full Text] [Related]
13. MPEXS-DNA, a new GPU-based Monte Carlo simulator for track structures and radiation chemistry at subcellular scale.
Okada S; Murakami K; Incerti S; Amako K; Sasaki T
Med Phys; 2019 Mar; 46(3):1483-1500. PubMed ID: 30593679
[TBL] [Abstract][Full Text] [Related]
14. Application of Site-Identification by Ligand Competitive Saturation in Computer-Aided Drug Design.
Goel H; Hazel A; Yu W; Jo S; MacKerell AD
New J Chem; 2022 Jan; 46(3):919-932. PubMed ID: 35210743
[TBL] [Abstract][Full Text] [Related]
15. Enhancing Water Sampling in Free Energy Calculations with Grand Canonical Monte Carlo.
Ross GA; Russell E; Deng Y; Lu C; Harder ED; Abel R; Wang L
J Chem Theory Comput; 2020 Oct; 16(10):6061-6076. PubMed ID: 32955877
[TBL] [Abstract][Full Text] [Related]
16. Molecular simulations of confined liquids: an alternative to the grand canonical Monte Carlo simulations.
Ghoufi A; Morineau D; Lefort R; Hureau I; Hennous L; Zhu H; Szymczyk A; Malfreyt P; Maurin G
J Chem Phys; 2011 Feb; 134(7):074104. PubMed ID: 21341825
[TBL] [Abstract][Full Text] [Related]
17. DICE: A Monte Carlo Code for Molecular Simulation Including the Configurational Bias Monte Carlo Method.
Cezar HM; Canuto S; Coutinho K
J Chem Inf Model; 2020 Jul; 60(7):3472-3488. PubMed ID: 32470296
[TBL] [Abstract][Full Text] [Related]
18. Comparison of Grand Canonical and Conventional Molecular Dynamics Simulation Methods for Protein-Bound Water Networks.
Ekberg V; Samways ML; Misini Ignjatović M; Essex JW; Ryde U
ACS Phys Chem Au; 2022 May; 2(3):247-259. PubMed ID: 35637786
[TBL] [Abstract][Full Text] [Related]
19. New capabilities of the Monte Carlo dose engine ARCHER-RT: Clinical validation of the Varian TrueBeam machine for VMAT external beam radiotherapy.
Adam DP; Liu T; Caracappa PF; Bednarz BP; Xu XG
Med Phys; 2020 Jun; 47(6):2537-2549. PubMed ID: 32175615
[TBL] [Abstract][Full Text] [Related]
20. Thermodynamics and partitioning of homopolymers into a slit-A grand canonical Monte Carlo simulation study.
Jiang W; Wang Y
J Chem Phys; 2004 Aug; 121(8):3905-13. PubMed ID: 15303959
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]
