Heterogeneity in structure and dynamics of water near bilayers using TIP3P and TIP4P/2005 water models
Sign Up to like & getrecommendations! Published in 2019 at "Chemical Physics"
DOI: 10.1016/j.chemphys.2019.110396
Abstract: Abstract Capturing structure and dynamics of both lipids and water near membranes using simulations as in experiments is a challenging task till date. Dimyristoylphophatidylcholine (DMPC) lipid bilayers with Berger and CHARMM36 force-fields have been investigated… read more here.
Keywords: water; tip4p 2005; tip3p tip4p; water near ... See more keywords
Computational investigation of the conformation transitions of DNA in modified water models
Sign Up to like & getrecommendations! Published in 2018 at "Journal of Molecular Liquids"
DOI: 10.1016/j.molliq.2018.08.129
Abstract: Abstract Modified water models with different bond length are used to investigate solvent activity effects on DNA structure. The dodecamer d(CGCGAATTCGCG) DNA segment is merged into the different model solvents and its conformation transition is… read more here.
Keywords: dna; conformation; activity; water models ... See more keywords
Bottom-Up Informed and Iteratively Optimized Coarse-Grained Non-Markovian Water Models with Accurate Dynamics
Sign Up to like & getrecommendations! Published in 2023 at "Journal of Chemical Theory and Computation"
DOI: 10.1021/acs.jctc.2c00871
Abstract: Molecular dynamics (MD) simulations based on coarse-grained (CG) particle models of molecular liquids generally predict accelerated dynamics and misrepresent the time scales for molecular vibrations and diffusive motions. The parametrization of Generalized Langevin Equation (GLE)… read more here.
Keywords: water models; bottom informed; water; informed iteratively ... See more keywords
Energetics of water proton configurations in gas hydrates: comparison of various water models
Sign Up to like & getrecommendations! Published in 2018 at "Molecular Simulation"
DOI: 10.1080/08927022.2017.1383990
Abstract: Abstract The total interaction energies for a large number of water proton configurations in the unit cell of hydrate structure I consisting of 46 molecules are compared for qualitatively different water models, such as SPC/E,… read more here.
Keywords: proton configurations; water proton; water; energetics water ... See more keywords