Bridging the gap between thermodynamic integration and umbrella sampling provides a novel analysis method: "Umbrella integration".
نویسندگان
چکیده
We present a method to analyze biased molecular-dynamics and Monte Carlo simulations, also known as umbrella sampling. In the limiting case of a strong bias, this method is equivalent to thermodynamic integration. It employs only quantities with easily controllable equilibration and greatly reduces the statistical errors compared to the standard weighted histogram analysis method. We show the success of our approach for two examples, one analytic function, and one biological system.
منابع مشابه
Umbrella sampling
The calculation of free-energy differences is one of the main challenges in computational biology and biochemistry. Umbrella sampling, biased molecular dynamics (MD), is one of the methods that provide free energy along a reaction coordinate. Here, the method is derived in a historic overview and is compared with related methods like thermodynamic integration, slow growth, steered MD, or the Ja...
متن کاملEvaluation of the Adaptive Umbrella Sampling Method
(Received December, 1988) The adaptive umbrella sampling technique, introduced recently to improve the probability ratio method and found to perform more reliably then the customary harmonic umbrella sampling, is tested and compared with other free energy methods. One of the tests applies the method to a transition involving a chemical change: calculation of the hydration free energy difference...
متن کاملNucleation of liquid bridges and bubbles in nanoscale capillaries
Nucleation of liquid bridges and bubbles during condensation and evaporation of Lennard-Jones fluid in cylindrical pores is explored by Monte Carlo simulation. The isotherm of constrained critical nuclei is constructed using the gauge cell method. We confirm the Everett–Haynes scenario of bridging through the formation of a bump/undulation on the adsorption film. The molecular structure of grow...
متن کاملAnalysis of the statistical error in umbrella sampling simulations by umbrella integration.
Umbrella sampling simulations, or biased molecular dynamics, can be used to calculate the free-energy change of a chemical reaction. We investigate the sources of different sampling errors and derive approximate expressions for the statistical errors when using harmonic restraints and umbrella integration analysis. This leads to generally applicable rules for the choice of the bias potential an...
متن کاملMolecular dynamics simulations in the grand canonical ensemble: Formulation of a bias potential for umbrella sampling
An extended Hamiltonian technique for performing grand canonical ensemble molecular dynamics simulations has been reformulated to include umbrella sampling, thus improving the efficiency of particle creation and annihilation processes. This was accomplished through incorporation of a bias potential in the Hamiltonian that modifies the free energy contour between integer particle number states. ...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
عنوان ژورنال:
- The Journal of chemical physics
دوره 123 14 شماره
صفحات -
تاریخ انتشار 2005