Constant temperature simulations using the Langevin equation with velocity Verlet integration

Paterlini, Marta; Ferguson, David M.

doi:10.1016/s0301-0104(98)00214-6

Cited by 190 publications

(140 citation statements)

References 15 publications

Supporting

Mentioning

138

Contrasting

Order By: Relevance

“…Simulations were carried out in the NVT ensemble with a reference temperature of 298 K and the LangevinVerlet integrator. 40 In the OSBS reaction, at the first step, the PMF was performed exploring the reaction coordinate with a window width of 0.03 Å, and at the second step (a bidimensional PMF) with a window width of 0.05 Å (the total number of windows were 100 and 1600, respectively). At the first step of the NAAAR reaction, the reaction coordinate was then explored with a window width of 0.05 Å, and at the second step the reaction coordinate was explored with a window width of 0.03 Å.…”

Section: Free Energy Calculationsmentioning

confidence: 99%

Enzyme Promiscuity in Enolase Superfamily. Theoretical Study of o-Succinylbenzoate Synthase Using QM/MM Methods

et al. 2015

View full text Add to dashboard Cite

The promiscuous activity of the enzyme o-Succinylbenzoate Synthase (OSBS) from the actinobacteria Amycolatopsis is investigated by means of QM/MM methods, using both Density Functional Theory and Semiempirical Hamiltonians. This enzyme catalyzes not only the dehydration of 2-succinyl-6R-hydroxy-2,4-cyclohexadiene-1R-carboxylate but also catalyzes racemization of different acylaminoacids, being N-succinyl-Rphenylglycine the best substrate. We investigated the molecular mechanisms for both reactions exploring the Potential Energy Surface. Then, Molecular Dynamics simulations were performed to obtain the free energy profiles and the averaged interaction energies of enzymatic residues with the reacting system. Our results confirm the plausibility of the reaction mechanisms proposed in the literature, with a good agreement between theoretical and experimentally-derived activation free energies. Our simulations unravel the role played by the different residues in each of the two possible reactions. The presence of flexible loops in the active site and the selection of structural modifications in the substrate seem to be key elements to promote the promiscuity of this enzyme.

show abstract

Section: Free Energy Calculationsmentioning

confidence: 99%

Enzyme Promiscuity in Enolase Superfamily. Theoretical Study of o-Succinylbenzoate Synthase Using QM/MM Methods

et al. 2015

View full text Add to dashboard Cite

show abstract

“…We use an approach in which the deterministic part of the equations of motion of the inner particles are handled by the use of the Verlet algorithm [30] so as to ensure that, in the absence of the heat baths, energy is conserved. For the equations of motion of the first and last particles, which contain the stochastic forces due to the heat baths, we used the stochastic Verlet algorithm developed in [31]. As for the stochastic shot noises we treat them as follows.…”

Section: Numerical Solutionsmentioning

confidence: 99%

Fourier's law from a chain of coupled anharmonic oscillators under energy-conserving noise

Landi

Oliveira

2013

Phys. Rev. E

View full text Add to dashboard Cite

We analyze the transport of heat along a chain of particles interacting through anharmonic potentials consisting of quartic terms in addition to harmonic quadratic terms and subject to heat reservoirs at its ends. Each particle is also subject to an impulsive shot noise with exponentially distributed waiting times whose effect is to change the sign of its velocity, thus conserving the energy of the chain. We show that the introduction of this energy conserving stochastic noise leads to Fourier's law. The behavior of thels heat conductivity for small intensities of the shot noise and large system sizes are found to obey a finite-size scaling relation. We also show that the heat conductivity is not constant but is an increasing monotonic function of temperature.

show abstract

“…[39]). Focusing on the framework of a so-called NPT-ensemble (fixed particle number, external pressure and temperature) we have done the simulations by applying Langevin temperature control [40] and NosØ-Hoover Langevin piston pressure control [40,41] (for more details see refs. [19,23]).…”

Section: Simulations and Dft/td-dft Calculationsmentioning

confidence: 99%

A Mixed Quantum–Classical Description of Excitation Energy Transfer in Supramolecular Complexes: Förster Theory and beyond

et al. 2011

View full text Add to dashboard Cite

Electronic excitation energy transfer (EET) is described theoretically for the chromophore complex P(4) formed by a butanediamine dendrimer to which four pheophorbide-a molecules are covalently linked. To achieve a description with atomic resolution, and to account for the effect of an ethanol solvent, a mixed quantum-classical methodology is utilized. Room-temperature molecular dynamics simulations are used to describe the nuclear dynamics, and EET is accounted for in utilizing a mixed quantum-classical formulation of the transition rates. Therefore, the full quantum expression of the EET rates is given and the change to a mixed quantum-classical version is briefly explained. The description results in the calculation of transition rates which coincide rather satisfactory with available experimental data on P(4). It is also shown that different assumptions of classical Förster theory are not valid for P(4). The temporal behavior of EET deduced from the rate equations is confronted with that following from the solution of the time-dependent Schrödinger equation entering the mixed quantum-classical description of EET. From this we can conclude that EET in flexible chromophore complexes such as P(4) can be rather satisfactory estimated by single transition rates. A correct description, however, is only achievable by using a sufficiently large set of rates that correspond to the various possible equilibrium configurations of the complex.

show abstract

Constant temperature simulations using the Langevin equation with velocity Verlet integration

Cited by 190 publications

References 15 publications

Enzyme Promiscuity in Enolase Superfamily. Theoretical Study of o-Succinylbenzoate Synthase Using QM/MM Methods

Enzyme Promiscuity in Enolase Superfamily. Theoretical Study of o-Succinylbenzoate Synthase Using QM/MM Methods

Fourier's law from a chain of coupled anharmonic oscillators under energy-conserving noise

A Mixed Quantum–Classical Description of Excitation Energy Transfer in Supramolecular Complexes: Förster Theory and beyond

Contact Info

Product

Resources

About