Thermostat Algorithms for Molecular Dynamics Simulations

Hünenberger, Philippe H.

doi:10.1007/b99427

Cited by 472 publications

(348 citation statements)

References 121 publications

(237 reference statements)

Supporting

Mentioning

337

Contrasting

Unclassified

Order By: Relevance

“…He established the mathematical formulation of the so called Nosé-Hoover thermostat [32][33][34][35][36][37] enabling the molecular dynamics simulation of a system to sample configurations of a canonical (constant-temperature) ensemble. It is based on the extension of the real system by an artificial dynamical time scaling variable s. This important relationship serves in the following for the establishment of the microscopic entropy of a single particle (note, that s n is the discrete analog of s).…”

Section: Scaling Of Time In Accordance To Nosémentioning

confidence: 99%

“…While this equation is in principle reversible, it is interesting to note, that it could be irreversible if the friction term is constrained to values 0. The ad hoc introduction of such a friction term is often used in classical mechanics to introduce irreversibility, stochastisity or/and to deal with the interaction of the system of interest with its surrounding as exemplified for example by the Langevin dynamics [5,37]. It is also used to describe and study the quantum mechanical decoherence phenomenon [38].…”

Section: Scaling Of Time In Accordance To Nosémentioning

confidence: 99%

“…Following Nosé [22,37] from the Lagrangian (Equation (22)) in the disca representation the corresponding Hamiltonian can now be writ…”

Section: The Microscopic Entropy Of a Single Particlementioning

confidence: 99%

“…Nosé and Hoover figured that the equations of motion can be reformulated to go back to a representation that has a homogenous time sampling yielding the disco representation defined in Figure 2 [32,33,37]. The transformation from the disca system to the disco system variables is thereby achieved through r n =r n ,ṙ n =ṙ nsn ,s n = s n , F (r n ) = F (r n ) ,ṡ n =s nṡn ,…”

Section: The Microscopic Entropy Of a Single Particlementioning

confidence: 99%

See 3 more Smart Citations

A Derivation of a Microscopic Entropy and Time Irreversibility From the Discreteness of Time

Riek

2014

Entropy

View full text Add to dashboard Cite

The basic microsopic physical laws are time reversible. In contrast, the second law of thermodynamics, which is a macroscopic physical representation of the world, is able to describe irreversible processes in an isolated system through the change of entropy S > 0. It is the attempt of the present manuscript to bridge the microscopic physical world with its macrosocpic one with an alternative approach than the statistical mechanics theory of Gibbs and Boltzmann. It is proposed that time is discrete with constant step size. Its consequence is the presence of time irreversibility at the microscopic level if the present force is of complex nature (F (r) = const). In order to compare this discrete time irreversible mechamics (for simplicity a "classical", single particle in a one dimensional space is selected) with its classical Newton analog, time reversibility is reintroduced by scaling the time steps for any given time step n by the variable s n leading to the Nosé-Hoover Lagrangian. The corresponding Nosé-Hoover Hamiltonian comprises a term N df k B T ln s n (k B the Boltzmann constant, T the temperature, and N df the number of degrees of freedom) which is defined as the microscopic entropyS n at time point n multiplied by T . Upon ensemble averaging this microscopic entropy S n in equilibrium for a system which does not have fast changing forces approximates its macroscopic counterpart known from thermodynamics. The presented derivation with the resulting analogy between the ensemble averaged microscopic entropy and its thermodynamic analog suggests that the original description of the entropy by Boltzmann and Gibbs is just an ensemble averaging of the time scaling variable s n which is in equilibrium close to 1, but that the entropy term itself has its root not in statistical mechanics but rather in the discreteness of time.

show abstract

Section: Scaling Of Time In Accordance To Nosémentioning

confidence: 99%

Section: Scaling Of Time In Accordance To Nosémentioning

confidence: 99%

“…Following Nosé [22,37] from the Lagrangian (Equation (22)) in the disca representation the corresponding Hamiltonian can now be writ…”

Section: The Microscopic Entropy Of a Single Particlementioning

confidence: 99%

Section: The Microscopic Entropy Of a Single Particlementioning

confidence: 99%

See 2 more Smart Citations

A Derivation of a Microscopic Entropy and Time Irreversibility From the Discreteness of Time

Riek

2014

Entropy

View full text Add to dashboard Cite

show abstract

“…Utilization of a single thermostat for temperature control in these solute-solvent systems leads to differences between the solvent and solute temperatures, an effect called "hot solvent -cold solute problem" [10]. This problem is normally overcome by employing one thermostat for the proteins and another for the solvent [11]. However, it has recently been [12] reported that the small differences observed between the solute and solvent temperatures upon application of a sole thermostat are due to the way the temperature is calculated and a large difference in temperature indicates a problem in the methodology.…”

Section: Introductionmentioning

confidence: 99%

Effect of the thermostat in the molecular dynamics simulation on the folding of the model protein chignolin

Fuzo

Degrève

2011

J Mol Model

View full text Add to dashboard Cite

Molecular dynamics simulations of the model protein chignolin with explicit solvent were carried out, in order to analyze the influence of the Berendsen thermostat on the evolution and folding of the peptide. The dependence of the peptide behavior on temperature was tested with the commonly employed thermostat scheme consisting of one thermostat for the protein and another for the solvent. The thermostat coupling time of the protein was increased to infinity, when the protein is not in direct contact with the thermal bath, a situation known as minimally invasive thermostat. In agreement with other works, it was observed that only in the last situation the instantaneous temperature of the model protein obeys a canonical distribution. As for the folding studies, it was shown that, in the applications of the commonly utilized thermostat schemes, the systems are trapped in local minima regions from which it has difficulty escaping. With the minimally invasive thermostat the time that the protein needs to fold was reduced by two to three times. These results show that the obstacles to the evolution of the extended peptide to the folded structure can be overcome when the temperature of the peptide is not directly controlled.

show abstract

Molecular Dynamics Computations for Proteins: A Case Study in Membrane Ion Permeation

Allen

2009

Digital Encyclopedia of Applied Physics

View full text Add to dashboard Cite

Computer simulation can provide an atomic‐level view of protein structure and function that is unattainable with experiments alone. In this chapter, we demonstrate how molecular dynamics (MD) simulation can reveal the microscopic mechanisms of biomolecular activity. In particular, we illustrate the quantitative value of MD simulation by exploring ion channel proteins that allow selective permeation of charged molecules across cell membranes to control our nervous systems and chemical activity in the body. We begin by introducing the basic statistical mechanical formulation and methodological aspects of modern day MD simulations. We then discuss how to analyze a simulation to obtain mechanistic insight through calculation of various molecular properties. Special attention is given to quantitative thermodynamic calculations, which are the driving forces of protein function. We explain how to calculate free energies and equilibrium constants using potential of mean force (PMF) and free energy perturbation (FEP) techniques as well as the use of more advanced sampling approaches. These methods are then used to study ion permeation through the gramicidin A (gA) channel as well as the energetics of arginine side chain translocation across a lipid bilayer to assess models of voltage‐gated ion channel activation.

show abstract

Thermostat Algorithms for Molecular Dynamics Simulations

Cited by 472 publications

References 121 publications

A Derivation of a Microscopic Entropy and Time Irreversibility From the Discreteness of Time

A Derivation of a Microscopic Entropy and Time Irreversibility From the Discreteness of Time

Effect of the thermostat in the molecular dynamics simulation on the folding of the model protein chignolin

Molecular Dynamics Computations for Proteins: A Case Study in Membrane Ion Permeation

Contact Info

Product

Resources

About