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Themed collection Insights from advanced methods in molecular dynamics

13 articles
Perspective

Elucidation of the conformational dynamics of multi-body systems by construction of Markov state models

Recent algorithmic progresses in Markov State Model construction that enable optimal state definition and efficient estimation of the slow uphill kinetics are expected to boost investigations of complex multi-body processes.

Graphical abstract: Elucidation of the conformational dynamics of multi-body systems by construction of Markov state models
Open Access Communication

On the calculation of equilibrium thermodynamic properties from molecular dynamics

We explain the necessity of performing ensemble simulations to compute macroscopic properties in classical molecular dynamics simulation.

Graphical abstract: On the calculation of equilibrium thermodynamic properties from molecular dynamics
Paper

Lipid molecules can induce an opening of membrane-facing tunnels in cytochrome P450 1A2

The structure and dynamics of the membrane-bound full-length human cytochrome P450 1A2 (CYP1A2) in aqueous solution determined by coarse-grained and all-atom molecular dynamics simulations.

Graphical abstract: Lipid molecules can induce an opening of membrane-facing tunnels in cytochrome P450 1A2
Paper

The i-TTM model for ab initio-based ion–water interaction potentials. II. Alkali metal ion–water potential energy functions

A new set of i-TTM potential energy functions describing the interactions between alkali metal ions and water molecules is reported.

Graphical abstract: The i-TTM model for ab initio-based ion–water interaction potentials. II. Alkali metal ion–water potential energy functions
Paper

Simulations of the water exchange dynamics of lanthanide ions in 1-ethyl-3-methylimidazolium ethyl sulfate ([EMIm][EtSO4]) and water

Molecular dynamics simulations have been carried out to explain the water-exchange rates of lanthanide ions in water and water/[EMIm][EtSO4] observed from 17O-NMR experiments. Our simulations are in agreement with experimental results with respect to water-exchange trends.

Graphical abstract: Simulations of the water exchange dynamics of lanthanide ions in 1-ethyl-3-methylimidazolium ethyl sulfate ([EMIm][EtSO4]) and water
Paper

Toward polarizable AMOEBA thermodynamics at fixed charge efficiency using a dual force field approach: application to organic crystals

First principles prediction of the structure, thermodynamics and solubility of organic molecular crystals, which play a central role in chemical, material, pharmaceutical and engineering sciences, challenges both potential energy functions and sampling methodologies.

Graphical abstract: Toward polarizable AMOEBA thermodynamics at fixed charge efficiency using a dual force field approach: application to organic crystals
Paper

Rationalising pKa shifts in Bacillus circulans xylanase with computational studies

Molecular mechanism for pKa shifts for the key residues in wild-type and mutants of BcX based on three different computational methods.

Graphical abstract: Rationalising pKa shifts in Bacillus circulans xylanase with computational studies
Open Access Paper

Getting excited: challenges in quantum-classical studies of excitons in polymeric systems

A combination of classical molecular dynamics (MM/MD) and quantum chemical calculations based on the density functional theory (DFT) and many-body Green's functions theory (GW-BSE) was performed to describe the conformational and optical properties of diphenylethyne (DPE), methylated-DPE and poly para phenylene ethynylene (PPE).

Graphical abstract: Getting excited: challenges in quantum-classical studies of excitons in polymeric systems
Paper

Reaction mechanism of the dengue virus serine protease: a QM/MM study

The dengue virus (DENV) is the causative agent of the viral infection dengue fever. It utilizes the NS2B-NS3pro serine protease to cleave the viral polyprotein into its constituents. We present here a QM/MM to study of the first step (acylation) of the reaction catalyzed by NS2B-NS3pro, using PDDG/PM3 for the QM subsystem, and Amber ff99SB for the MM subsystem.

Graphical abstract: Reaction mechanism of the dengue virus serine protease: a QM/MM study
Paper

Lagrangian descriptors in dissipative systems

In noisy chemical reactions with dissipation a reweighted Lagrangian descriptor reveals invariant manifolds.

Graphical abstract: Lagrangian descriptors in dissipative systems
Paper

Transition state geometry of driven chemical reactions on time-dependent double-well potentials

The minimum contour in the forward Lagrangian descriptor overlaps the invariant manifold (in green) dividing reactant and product regions.

Graphical abstract: Transition state geometry of driven chemical reactions on time-dependent double-well potentials
Paper

Calculating binding free energies of host–guest systems using the AMOEBA polarizable force field

Cucurbit[7]uril host–guest binding free energies are investigated using the AMOEBA polarizable force field.

Graphical abstract: Calculating binding free energies of host–guest systems using the AMOEBA polarizable force field
Open Access Correction

Correction: Simulations of the water exchange dynamics of lanthanide ions in 1-ethyl-3-methylimidazolium ethyl sulfate ([EMIm][EtSO4]) and water

13 articles

About this collection

Molecular dynamics (MD) simulations are nowadays routinely used to complement experimental results and to predict properties or behaviours of myriad systems. Recent advances on the development of algorithms and potentials have broadened the applicability of MD calculations. This issue of PCCP aims to highlight the new insights and applications that have been enabled by the use of advanced MD techniques and potentials. The issue is guest-edited by G. Andres Cisneros (Wayne State University), Haiyan Liu (University of Science & Technology of China), Jean-Philip Piquemal (Sorbonne Université) and Pengyu Ren (University of Texas at Austin).

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