189 related articles for article (PubMed ID: 26636365)
1. Ensuring Mixing Efficiency of Replica-Exchange Molecular Dynamics Simulations.
Abraham MJ; Gready JE
J Chem Theory Comput; 2008 Jul; 4(7):1119-28. PubMed ID: 26636365
[TBL] [Abstract][Full Text] [Related]
2. Improved Efficiency of Replica Exchange Simulations through Use of a Hybrid Explicit/Implicit Solvation Model.
Okur A; Wickstrom L; Layten M; Geney R; Song K; Hornak V; Simmerling C
J Chem Theory Comput; 2006 Mar; 2(2):420-33. PubMed ID: 26626529
[TBL] [Abstract][Full Text] [Related]
3. Convergence and sampling efficiency in replica exchange simulations of peptide folding in explicit solvent.
Periole X; Mark AE
J Chem Phys; 2007 Jan; 126(1):014903. PubMed ID: 17212515
[TBL] [Abstract][Full Text] [Related]
4. Improving the replica-exchange molecular-dynamics method for efficient sampling in the temperature space.
Chen C; Xiao Y; Huang Y
Phys Rev E Stat Nonlin Soft Matter Phys; 2015 May; 91(5):052708. PubMed ID: 26066200
[TBL] [Abstract][Full Text] [Related]
5. Convergence of replica exchange molecular dynamics.
Zhang W; Wu C; Duan Y
J Chem Phys; 2005 Oct; 123(15):154105. PubMed ID: 16252940
[TBL] [Abstract][Full Text] [Related]
6. Influence of various parameters in the replica-exchange molecular dynamics method: Number of replicas, replica-exchange frequency, and thermostat coupling time constant.
Iwai R; Kasahara K; Takahashi T
Biophys Physicobiol; 2018; 15():165-172. PubMed ID: 30250775
[TBL] [Abstract][Full Text] [Related]
7. On the use of a weak-coupling thermostat in replica-exchange molecular dynamics simulations.
Lin Z; van Gunsteren WF
J Chem Phys; 2015 Jul; 143(3):034110. PubMed ID: 26203017
[TBL] [Abstract][Full Text] [Related]
8. How Efficient Is Replica Exchange Molecular Dynamics? An Analytic Approach.
Nymeyer H
J Chem Theory Comput; 2008 Apr; 4(4):626-36. PubMed ID: 26620937
[TBL] [Abstract][Full Text] [Related]
9. Efficient Conformational Sampling in Explicit Solvent Using a Hybrid Replica Exchange Molecular Dynamics Method.
Chaudhury S; Olson MA; Tawa G; Wallqvist A; Lee MS
J Chem Theory Comput; 2012 Feb; 8(2):677-87. PubMed ID: 26596615
[TBL] [Abstract][Full Text] [Related]
10. Hamiltonian replica exchange molecular dynamics using soft-core interactions.
Hritz J; Oostenbrink C
J Chem Phys; 2008 Apr; 128(14):144121. PubMed ID: 18412437
[TBL] [Abstract][Full Text] [Related]
11. Optimization of replica exchange molecular dynamics by fast mimicking.
Hritz J; Oostenbrink C
J Chem Phys; 2007 Nov; 127(20):204104. PubMed ID: 18052416
[TBL] [Abstract][Full Text] [Related]
12. Replica-Exchange Methods for Biomolecular Simulations.
Sugita Y; Kamiya M; Oshima H; Re S
Methods Mol Biol; 2019; 2022():155-177. PubMed ID: 31396903
[TBL] [Abstract][Full Text] [Related]
13. Conformational space search of Neuromedin C using replica exchange molecular dynamics and molecular dynamics.
Sharma P; Singh P; Bisetty K; Rodriguez A; Perez JJ
J Pept Sci; 2011 Mar; 17(3):174-83. PubMed ID: 20878681
[TBL] [Abstract][Full Text] [Related]
14. Increasing the sampling efficiency of protein conformational transition using velocity-scaling optimized hybrid explicit/implicit solvent REMD simulation.
Yu Y; Wang J; Shao Q; Shi J; Zhu W
J Chem Phys; 2015 Mar; 142(12):125105. PubMed ID: 25833612
[TBL] [Abstract][Full Text] [Related]
15. Enhancing Conformation and Protonation State Sampling of Hen Egg White Lysozyme Using pH Replica Exchange Molecular Dynamics.
Swails JM; Roitberg AE
J Chem Theory Comput; 2012 Nov; 8(11):4393-404. PubMed ID: 26605601
[TBL] [Abstract][Full Text] [Related]
16. Large-scale asynchronous and distributed multidimensional replica exchange molecular simulations and efficiency analysis.
Xia J; Flynn WF; Gallicchio E; Zhang BW; He P; Tan Z; Levy RM
J Comput Chem; 2015 Sep; 36(23):1772-85. PubMed ID: 26149645
[TBL] [Abstract][Full Text] [Related]
17. Infinite swapping replica exchange molecular dynamics leads to a simple simulation patch using mixture potentials.
Lu J; Vanden-Eijnden E
J Chem Phys; 2013 Feb; 138(8):084105. PubMed ID: 23464138
[TBL] [Abstract][Full Text] [Related]
18. Exchange frequency in replica exchange molecular dynamics.
Sindhikara D; Meng Y; Roitberg AE
J Chem Phys; 2008 Jan; 128(2):024103. PubMed ID: 18205439
[TBL] [Abstract][Full Text] [Related]
19. Replica exchange simulation method using temperature and solvent viscosity.
Nguyen PH
J Chem Phys; 2010 Apr; 132(14):144109. PubMed ID: 20405987
[TBL] [Abstract][Full Text] [Related]
20. Walking freely in the energy and temperature space by the modified replica exchange molecular dynamics method.
Chen C; Huang Y
J Comput Chem; 2016 Jun; 37(17):1565-75. PubMed ID: 27059441
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]