Efficacy of independence sampling in replica exchange simulations of ordered and disordered proteins
Sign Up to like & getrecommendations! Published in 2017 at "Journal of Computational Chemistry"
DOI: 10.1002/jcc.24923
Abstract: Recasting temperature replica exchange (T‐RE) as a special case of Gibbs sampling has led to a simple and efficient scheme for enhanced mixing (Chodera and Shirts, J. Chem. Phys., 2011, 135, 194110). To critically examine… read more here.
Keywords: independence sampling; replica exchange; simulations ordered; ordered disordered ... See more keywords
Simulation studies of polypeptoids using replica exchange with dynamical scaling and dihedral biasing
Sign Up to like & getrecommendations! Published in 2022 at "Journal of Computational Chemistry"
DOI: 10.1002/jcc.26887
Abstract: Polypeptoids differ from polypeptides in that the amide bond can more frequently adopt both cis and trans conformations. The transition between the two conformations requires overcoming a large energy barrier, making it difficult for conventional… read more here.
Keywords: replica exchange; replica; simulation studies; amide bond ... See more keywords
Acceleration of generalized replica exchange with solute tempering simulations of large biological systems on massively parallel supercomputer.
Sign Up to like & getrecommendations! Published in 2023 at "Journal of computational chemistry"
DOI: 10.1002/jcc.27124
Abstract: Generalized replica exchange with solute tempering (gREST) is one of the enhanced sampling algorithms for proteins or other systems with rugged energy landscapes. Unlike the replica-exchange molecular dynamics (REMD) method, solvent temperatures are the same… read more here.
Keywords: replica exchange; generalized replica; exchange solute; exchange ... See more keywords
Optimization of replica exchange temperature ladder under the well-tempered ensemble
Sign Up to like & getrecommendations! Published in 2018 at "Chemical Physics Letters"
DOI: 10.1016/j.cplett.2018.09.036
Abstract: Abstract Selection of temperature sequence and bias factor is a critical step for the preparation of Parallel Tempering simulations in a Well-Tempered Ensemble (PT-WTE). We provide a scheme in this study to generate the temperature… read more here.
Keywords: temperature; optimization replica; well tempered; replica exchange ... See more keywords
A two-dimensional replica-exchange molecular dynamics method for simulating RNA folding using sparse experimental restraints.
Sign Up to like & getrecommendations! Published in 2019 at "Methods"
DOI: 10.1016/j.ymeth.2019.05.001
Abstract: We present a 2D replica exchange protocol incorporating secondary structure information to dramatically improve 3D RNA folding using molecular dynamics simulations. We show that incorporating base-pairing restraints into all-atom, explicit solvent simulations enables the accurate… read more here.
Keywords: molecular dynamics; replica exchange; rna; rna folding ... See more keywords
Binding of Antimicrobial Peptide Indolicidin to DMPC Bilayer Using Replica-Exchange Molecular Dynamics
Sign Up to like & getrecommendations! Published in 2025 at "Journal of Chemical Information and Modeling"
DOI: 10.1021/acs.jcim.5c01153
Abstract: Cationic antimicrobial peptides (AMPs) are toxic to microbes, such as bacteria and fungi, and have been increasingly studied as an alternative to traditional antibiotics, in part because AMPs are bactericidal with a minimum risk of… read more here.
Keywords: exchange molecular; indolicidin; dmpc bilayer; molecular dynamics ... See more keywords
Accelerating the Ensemble Convergence of RNA Hairpin Simulations with a Replica Exchange Structure Reservoir.
Sign Up to like & getrecommendations! Published in 2022 at "Journal of chemical theory and computation"
DOI: 10.1021/acs.jctc.2c00065
Abstract: RNA is a key participant in many biological processes, but studies of RNA using computer simulations lag behind those of proteins, largely due to less-developed force fields and the slow dynamics of RNA. Generating converged… read more here.
Keywords: replica exchange; structure; rna; ensemble convergence ... See more keywords
Re-Balancing Replica Exchange with Solute Tempering for Sampling Dynamic Protein Conformations.
Sign Up to like & getrecommendations! Published in 2023 at "Journal of chemical theory and computation"
DOI: 10.1021/acs.jctc.2c01139
Abstract: Replica exchange with solute tempering (REST) is a highly effective variant of replica exchange for enhanced sampling in explicit solvent simulations of biomolecules. By scaling the Hamiltonian for a selected "solute" region of the system,… read more here.
Keywords: replica exchange; exchange solute; exchange; solute solvent ... See more keywords
Alchemical Free Energy and Hamiltonian Replica Exchange Molecular Dynamics to Compute Hydrofluorocarbon Isotherms in Imidazolium-Based Ionic Liquids.
Sign Up to like & getrecommendations! Published in 2023 at "Journal of chemical theory and computation"
DOI: 10.1021/acs.jctc.3c00206
Abstract: Ionic liquids (ILs) have shown promise for applications that leverage differential gas solubility in an IL solvent, e.g., gas separations. Although most available literature provides Henry's law constants, the ability to efficiently estimate full isotherms… read more here.
Keywords: replica exchange; solubility; energy; hamiltonian replica ... See more keywords
Multiple Parameter Replica Exchange Gaussian Accelerated Molecular Dynamics for Enhanced Sampling and Free Energy Calculation of Biomolecular Systems.
Sign Up to like & getrecommendations! Published in 2024 at "Journal of chemical theory and computation"
DOI: 10.1021/acs.jctc.4c00501
Abstract: This study introduces a novel method named multiple parameter replica exchange Gaussian accelerated molecular dynamics (MP-Rex-GaMD), building on the Gaussian accelerated molecular dynamics (GaMD) algorithm. GaMD enhances sampling and retrieves free energy information for biomolecular… read more here.
Keywords: energy; gaussian accelerated; free energy; molecular dynamics ... See more keywords
Replica Exchange Nested Sampling
Sign Up to like & getrecommendations! Published in 2025 at "Journal of Chemical Theory and Computation"
DOI: 10.1021/acs.jctc.5c00588
Abstract: Nested sampling (NS) has emerged as a powerful tool for exploring thermodynamic properties in materials science. However, its efficiency is often hindered by the limitations of Markov chain Monte Carlo (MCMC) sampling. In strongly multimodal… read more here.
Keywords: exchange nested; replica exchange; nested sampling; exchange ... See more keywords