A molecular dynamics method for simulations in the canonical ensemble

Nosé, Shūichi

doi:10.1080/00268978400101201

Cited by 8,355 publications

(3,930 citation statements)

References 17 publications

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“…The Nosé-Hoover thermostat 39,40 was applied to control the temperature at 298 K, while the normal pressure was kept at 1 bar using the semi-isotropic form of the Parrinello-Rahman barostat 41 . The interfacial systems were constructed by first equilibrating two separate boxes containing the water and organic liquids with the same cross-sectional dimensions.…”

Section: Simulation Methodsmentioning

confidence: 99%

Molecular Dynamics Study of the Interface between Water and 2-Nitrophenyl Octyl Ether

Jorge

Cordeiro

2008

J. Phys. Chem. B

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We present results of molecular dynamics simulations of the interface between water and 2-nitrophenyloctyl ether (NPOE). This system is analyzed in detail using a procedure to calculate intrinsic profiles of several important properties (density, radial distribution functions, hydrogen bonds, molecular orientation, self-diffusion). The interface was found to be molecularly sharp, but corrugated by thermal fluctuations. Using a method based on capillary wave theory, we have estimated the interfacial tension and obtained good agreement with values calculated from the virial route. The results were compared to simulations of the water/nitrobenzene interface. The presence of an alkyl chain in NPOE introduces an added degree of hydrophobicity, which causes an increase in the interfacial tension. Furthermore, interfacial NPOE molecules are less organized than nitrobenzene and show a distinct dynamic response. These results shed light on the observed differences between these two organic liquids in electrochemical studies.

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Section: Simulation Methodsmentioning

confidence: 99%

Molecular Dynamics Study of the Interface between Water and 2-Nitrophenyl Octyl Ether

Jorge

Cordeiro

2008

J. Phys. Chem. B

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“…For completeness, a detailed simulation protocol is given in Table I. The MD-simulations are carried out in the NPT ensemble using the Nosé-Hoover thermostat [51,52] and the Rahman-Parrinello barostat [53,54] with coupling times τ T = 1.5 ps and τ p = 2.5 ps (assuming an isothermal compressibility of χ T = 4.5 10 −5 bar −1 ), respectively. The electrostatic interactions are treated in the "full potential" approach by the smooth particle mesh Ewald summation [55] with a real space cutoff of 0.9 nm and a mesh spacing of approximately 0.12 nm and 4th order interpolation.…”

Section: A MD Simulation Detailsmentioning

confidence: 99%

Low-temperature and high-pressure induced swelling of a hydrophobic polymer-chain in aqueous solution

Paschek

Nonn

Geiger

2005

Phys. Chem. Chem. Phys.

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We report molecular dynamics simulations of a hydrophobic polymer-chain in aqueous solution between 260 K and 420 K at pressures of 1 bar, 3000 bar, and 4500 bar. The simulations reveal a hydrophobically collapsed state at low pressures and high temperatures. At 3000 bar and about 260 K and at 4500 bar and about 260 K, however, a transition to a swelled state is observed. The transition is driven by a smaller volume and a remarkably strong lower enthalpy of the swelled state, indicating a steep positive slope of the corresponding transition line. The swelling is stabilized almost completely by the energetically favorable state of water in the polymers hydrophobic first hydration shell at low temperatures. Although surprising, this finding is consistent with the observation of a positive heat capacity of hydrophobic solvation. Moreover, the slope and location of the observed swelling transition for the collapsed hydrophobic chain coincides remarkably well with the cold denaturation transition of proteins.

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“…(6), is employed to obtain the required ensemble. Here, the detailed balance condition is described in terms of the amount of stochastic flow as follows:…”

Section: A Markov Chain Monte Carlo Methods With the Weight Allocationmentioning

confidence: 99%

“…To see usefulness of the Suwa-Todo algorithm for the replica-permutation method, we per- the Gaussian constraint method [4,5] to avoid the problem of non-ergodicity in the Nosé-Hoover thermostat [6][7][8] for the non-interacting particle system. The trajectory data were stored every 10.0 fs.…”

Section: A Asymmetric Double-well Potential Energymentioning

confidence: 99%

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Replica-Permutation Method with the Suwa–Todo Algorithm beyond the Replica-Exchange Method

Itoh

Okumura

2012

J. Chem. Theory Comput.

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We propose a new method for molecular dynamics and Monte Carlo simulations, which is referred to as the replica-permutation method (RPM), to realize more efficient sampling than the replicaexchange method (REM). In RPM not only exchanges between two replicas but also permutations among more than two replicas are performed. Furthermore, instead of the Metropolis algorithm, the Suwa-Todo algorithm is employed for replica-permutation trials to minimize its rejection ratio.We applied RPM to particles in a double-well potential energy, Met-enkephalin in vacuum, and a C-peptide analog of ribonuclease A in explicit water. For a comparison purposes, replica-exchange molecular dynamics simulations were also performed. As a result, RPM sampled not only the temperature space but also the conformational space more efficiently than REM for all systems.From our simulations of C-peptide, we obtained the α-helix structure with salt-bridges between Gly2 and Arg10 which is known in experiments. Calculating its free-energy landscape, the folding pathway was revealed from an extended structure to the α-helix structure with the salt-bridges.We found that the folding pathway consists of the two steps: The first step is the "salt-bridge formation step", and the second step is the "α-helix formation step". * Electronic address: itoh@ims.ac.jp † Electronic address: hokumura@ims.ac.jp

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A molecular dynamics method for simulations in the canonical ensemble

Cited by 8,355 publications

References 17 publications

Molecular Dynamics Study of the Interface between Water and 2-Nitrophenyl Octyl Ether

Molecular Dynamics Study of the Interface between Water and 2-Nitrophenyl Octyl Ether

Low-temperature and high-pressure induced swelling of a hydrophobic polymer-chain in aqueous solution

Replica-Permutation Method with the Suwa–Todo Algorithm beyond the Replica-Exchange Method

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