221 related articles for article (PubMed ID: 23477537)
1. Reliable oligonucleotide conformational ensemble generation in explicit solvent for force field assessment using reservoir replica exchange molecular dynamics simulations.
Henriksen NM; Roe DR; Cheatham TE
J Phys Chem B; 2013 Apr; 117(15):4014-27. PubMed ID: 23477537
[TBL] [Abstract][Full Text] [Related]
2. Accelerating the Ensemble Convergence of RNA Hairpin Simulations with a Replica Exchange Structure Reservoir.
Lam K; Kasavajhala K; Gunasekera S; Simmerling C
J Chem Theory Comput; 2022 Jun; 18(6):3930-3947. PubMed ID: 35502992
[TBL] [Abstract][Full Text] [Related]
3. Enhanced Conformational Sampling Using Replica Exchange with Collective-Variable Tempering.
Gil-Ley A; Bussi G
J Chem Theory Comput; 2015 Mar; 11(3):1077-85. PubMed ID: 25838811
[TBL] [Abstract][Full Text] [Related]
4. A convective replica-exchange method for sampling new energy basins.
Spill YG; Bouvier G; Nilges M
J Comput Chem; 2013 Jan; 34(2):132-40. PubMed ID: 22961200
[TBL] [Abstract][Full Text] [Related]
5. TIGER2: an improved algorithm for temperature intervals with global exchange of replicas.
Li X; Latour RA; Stuart SJ
J Chem Phys; 2009 May; 130(17):174106. PubMed ID: 19425768
[TBL] [Abstract][Full Text] [Related]
6. Enhanced conformational sampling of carbohydrates by Hamiltonian replica-exchange simulation.
Mishra SK; Kara M; Zacharias M; Koca J
Glycobiology; 2014 Jan; 24(1):70-84. PubMed ID: 24134878
[TBL] [Abstract][Full Text] [Related]
7. 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]
8. Boosting the conformational sampling by combining replica exchange with solute tempering and well-sliced metadynamics.
Kapakayala AB; Nair NN
J Comput Chem; 2021 Dec; 42(31):2233-2240. PubMed ID: 34585768
[TBL] [Abstract][Full Text] [Related]
9. Replica-Based Protein Structure Sampling Methods II: Advanced Hybrid Solvent TIGER2hs.
Geist N; Kulke M; Schulig L; Link A; Langel W
J Phys Chem B; 2019 Jul; 123(28):5995-6006. PubMed ID: 31265293
[TBL] [Abstract][Full Text] [Related]
10. Effect of the solvent on the conformational behavior of the alanine dipeptide deduced from MD simulations.
Rubio-Martinez J; Tomas MS; Perez JJ
J Mol Graph Model; 2017 Nov; 78():118-128. PubMed ID: 29055185
[TBL] [Abstract][Full Text] [Related]
11. Enhanced exchange algorithm without detailed balance condition for replica exchange method.
Kondo HX; Taiji M
J Chem Phys; 2013 Jun; 138(24):244113. PubMed ID: 23822233
[TBL] [Abstract][Full Text] [Related]
12. Estimating kinetic rates from accelerated molecular dynamics simulations: alanine dipeptide in explicit solvent as a case study.
de Oliveira CA; Hamelberg D; McCammon JA
J Chem Phys; 2007 Nov; 127(17):175105. PubMed ID: 17994855
[TBL] [Abstract][Full Text] [Related]
13. 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]
14. MuSTAR MD: multi-scale sampling using temperature accelerated and replica exchange molecular dynamics.
Yamamori Y; Kitao A
J Chem Phys; 2013 Oct; 139(14):145105. PubMed ID: 24116651
[TBL] [Abstract][Full Text] [Related]
15. Enhanced sampling of peptide and protein conformations using replica exchange simulations with a peptide backbone biasing-potential.
Kannan S; Zacharias M
Proteins; 2007 Feb; 66(3):697-706. PubMed ID: 17120231
[TBL] [Abstract][Full Text] [Related]
16. Coupling of replica exchange simulations to a non-Boltzmann structure reservoir.
Roitberg AE; Okur A; Simmerling C
J Phys Chem B; 2007 Mar; 111(10):2415-8. PubMed ID: 17300191
[TBL] [Abstract][Full Text] [Related]
17. Atomic-level characterization of the ensemble of the Aβ(1-42) monomer in water using unbiased molecular dynamics simulations and spectral algorithms.
Sgourakis NG; Merced-Serrano M; Boutsidis C; Drineas P; Du Z; Wang C; Garcia AE
J Mol Biol; 2011 Jan; 405(2):570-83. PubMed ID: 21056574
[TBL] [Abstract][Full Text] [Related]
18. Hamiltonian replica-permutation method and its applications to an alanine dipeptide and amyloid-β(29-42) peptides.
Itoh SG; Okumura H
J Comput Chem; 2013 Nov; 34(29):2493-7. PubMed ID: 23925979
[TBL] [Abstract][Full Text] [Related]
19. Hamiltonian replica exchange combined with elastic network analysis to enhance global domain motions in atomistic molecular dynamics simulations.
Ostermeir K; Zacharias M
Proteins; 2014 Dec; 82(12):3410-9. PubMed ID: 25243707
[TBL] [Abstract][Full Text] [Related]
20. The temperature intervals with global exchange of replicas empirical accelerated sampling method: parameter sensitivity and extension to a complex molecular system.
Li X; Latour RA
J Comput Chem; 2011 Apr; 32(6):1091-100. PubMed ID: 20949510
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]