Results 221 to 230 of about 83,346 (245)

Dynamic bond constraints in protein Langevin dynamics

The Journal of Chemical Physics, 2006
Bond constraint algorithms for molecular dynamics typically take, as the target constraint lengths, the values of the equilibrium bond lengths defined in the potential. In Langevin form, the equations of motion are temperature dependent, which gives the average value for the individual bond lengths a temperature dependence. In addition to this, locally
J, Franklin, S, Doniach
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Multidimensional Langevin modeling of biomolecular dynamics

The Journal of Chemical Physics, 2009
A systematic computational approach to describe the conformational dynamics of biomolecules in reduced dimensionality is presented. The method is based on (i) the decomposition of a high-dimensional molecular dynamics trajectory into a few “system” and (many) “bath” degrees of freedom and (ii) a Langevin simulation of the resulting model.
Hegger, Rainer, Stock, Gerhard
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Multidimensional Langevin Modeling of Nonoverdamped Dynamics

Physical Review Letters, 2015
Based on a given time series, data-driven Langevin modeling aims to construct a low-dimensional dynamical model of the underlying system. When dealing with physical data as provided by, e.g., all-atom molecular dynamics simulations, effects due to small damping may be important to correctly describe the statistics (e.g., the energy landscape) and the ...
Schaudinnus, Norbert, Bastian, Björn, Hegger, Rainer, Stock, Gerhard   +3 more
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Dynamical systems of Langevin type

Physica A: Statistical Mechanics and its Applications, 1996
Abstract Dynamical systems of Langevin type are deterministic mappings that arise if the Gaussian white noise of a Langevin equation is replaced by a deterministic chaotic dynamics. We describe the various types of mappings that can be obtained in this way, and investigate typical transition scenarios from complicated non-Gaussian to Langevin-like ...
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Langevin Equations and Non-Linear Dynamics

1995
For the modelling of stochastically behaving systems, apart from the master equation and the Fokker-Planck equation, often also stochastic differential equations are used (cf. [84]).
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Langevin and Generalised Langevin Dynamics

2007
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Constant pressure molecular dynamics simulation: The Langevin piston method

Journal of Chemical Physics, 1995
Richard W Pastor, Bernard R Brooks
exaly  

A simple and effective Verlet-type algorithm for simulating Langevin dynamics

Molecular Physics, 2013
Niels Grønbech-Jensen, Oded Farago
exaly  

A simple and accurate algorithm for path integral molecular dynamics with the Langevin thermostat

Journal of Chemical Physics, 2016
Jian Liu, Xinzijian Liu
exaly  

Langevin dynamics simulations of polymer translocation through nanopores

Journal of Chemical Physics, 2006
Ilkka Huopaniemi, Kaifu Luo, Tapio Ala-Nissila   +2 more
exaly