Molecular dynamics simulations with an implicit model of the solvent have allowed to investigate the reversible folding of structured peptides. For a 20-residue antiparallel beta-sheet peptide, the simulation results have revealed multiple folding pathways. Moreover, the conformational heterogeneity of the denatured state has been shown to originate from high enthalpy, high entropy basins with ...

Histone Nε-lysine methylation is a widespread posttranslational modification that is specifically recognised by a diverse class of Nε-methyllysine binding reader proteins. Combined thermodynamic data, molecular dynamics simulations, and quantum chemical studies reveal that reader proteins efficiently bind trimethylornithine and trimethylhomolysine, the simplest Nε-trimethyllysine analogues that...

While the determination of free-energy differences by MD simulation has become a standard procedure for which many techniques have been developed, total entropies and entropy differences are still hardly ever computed. An overview of techniques to determine entropy differences is given, and the accuracy and convergence behavior of five methods based on thermodynamic integration and perturbation...

Using molecular dynamic simulations, we study three families of continuous core-softened potentials consisting of two length scales: a shoulder scale and an attractive scale. All the families have the same slope between the two length scales but exhibit different potential energy gap between them. For each family three shoulder depths are analyzed. We show that all these systems exhibit a liqui...

Test-area deformations are used to analyze vapor-liquid interfaces of Lennard-Jones particles by molecular dynamics simulation. For planar vapor-liquid interfaces the change in free energy is captured by the average of the corresponding change in energy, the leading-order contribution. This is consistent with the commonly used mechanical (pressure-tensor) route for the surface tension. By contr...

We present molecular dynamics simulations of the extended simple-point-charge model of water to probe the dynamic properties at temperatures from 350 K down to 190 K and pressures from 2.5 GPa (25 kbar) down to -300 MPa (-3 kbar). We compare our results with those obtained experimentally, both of which show a diffusivity maximum as a function of pressure. We find that our simulation results are...

The kinetics and thermodynamics of an off-lattice model for a three-helix bundle protein are investigated as a function of a bias gap parameter that determines the energy difference between native and non-native contacts. A simple dihedral potential is used to introduce the tendency to form right-handed helices. For each value of the bias parameter, 100 trajectories of up to one microsecond are...

Steered molecular dynamics (SMD) permits efficient investigations of molecular processes by focusing on selected degrees of freedom. We explain how one can, in the framework of SMD, employ Jarzynski's equality (also known as the nonequilibrium work relation) to calculate potentials of mean force (PMF). We outline the theory that serves this purpose and connects nonequilibrium processes (such as...

We report the characterization of the energy landscape and the folding/unfolding thermodynamics of a hyperstable RNA tetraloop obtained through high-performance molecular dynamics simulations at microsecond timescales. Sampling of the configurational landscape is conducted using temperature replica exchange molecular dynamics over three isochores at high, ambient, and negative pressures to dete...

We show that evaporation from a quasistable molecular cluster may be treated as a kinetic problem involving the stochastically driven escape of a molecule from a potential of mean force. We derive expressions for the decay rate, and a relationship between the depth of the potential and the change in system free energy upon loss of a molecule from the cluster. This establishes a connection betwe...