Adiabatic Excited-State Molecular Dynamics with an Explicit Solvent: NEXMD-SANDER Implementation.
Sign Up to like & getrecommendations! Published in 2022 at "Journal of chemical theory and computation"
DOI: 10.1021/acs.jctc.2c00561
Abstract: We present a method to link the Nonadiabatic EXcited-state Molecular Dynamics (NEXMD) package to the SANDER package supplied by AMBERTOOLS to provide excited-state adiabatic quantum mechanics/molecular mechanics (QM/MM) simulations. NEXMD is a computational package particularly… read more here.
Keywords: state; molecular dynamics; nexmd sander; explicit solvent ... See more keywords
Comparison of Implicit and Explicit Solvent Models for the Calculation of Solvation Free Energy in Organic Solvents.
Sign Up to like & getrecommendations! Published in 2017 at "Journal of chemical theory and computation"
DOI: 10.1021/acs.jctc.7b00169
Abstract: Quantitative prediction of physical properties of liquids is important for many applications. Computational methods based on either explicit or implicit solvent models can be used to approximate thermodynamics properties of liquids. Here, we evaluate the… read more here.
Keywords: solvent models; explicit solvent; solvent; model ... See more keywords
Probing the accuracy of explicit solvent constant pH molecular dynamics simulations for peptides.
Sign Up to like & getrecommendations! Published in 2020 at "Journal of chemical theory and computation"
DOI: 10.1021/acs.jctc.9b01232
Abstract: Protonation states of titratable amino acids frequently play a key role in many biomolecular processes. Knowledge of protonatable residue charges at a given pH is essential for a correct understanding of protein catalysis, inter- and… read more here.
Keywords: accuracy explicit; constant molecular; explicit solvent; probing accuracy ... See more keywords
Reweighting of molecular simulations with explicit-solvent SAXS restraints elucidates ion-dependent RNA ensembles
Sign Up to like & getrecommendations! Published in 2021 at "Nucleic Acids Research"
DOI: 10.1093/nar/gkab459
Abstract: Abstract Small-angle X-ray scattering (SAXS) experiments are increasingly used to probe RNA structure. A number of forward models that relate measured SAXS intensities and structural features, and that are suitable to model either explicit-solvent effects… read more here.
Keywords: explicit solvent; saxs; rna; ion dependent ... See more keywords
Explicit solvent effects on macromolecular interactions from a solvent-augmented contact value theorem.
Sign Up to like & getrecommendations! Published in 2022 at "Physical review. E"
DOI: 10.1103/physreve.106.014608
Abstract: The Derjaguin-Landau-Verywey-Overbeek (DLVO) theory has been a remarkably accurate framework for the characterization of macromolecular stability in water solvent. In view of its solvent-implicit nature neglecting the electrostatics of water molecules with non-negligible charge structure… read more here.
Keywords: solvent augmented; value theorem; solvent; explicit solvent ... See more keywords
Implicit-solvent dissipative particle dynamics force field based on a four-to-one coarse-grained mapping scheme
Sign Up to like & getrecommendations! Published in 2018 at "PLoS ONE"
DOI: 10.1371/journal.pone.0198049
Abstract: A new set of efficient solvent-free dissipative particle dynamics (DPD) force fields was developed for phospholipids and peptides. To enhance transferability, this model maps around four heavy atoms and their connected hydrogen atoms into a… read more here.
Keywords: force field; particle dynamics; explicit solvent; coarse grained ... See more keywords