Free Energy Landscapes of Vesicle Fusion by Umbrella Sampling MD Simulations
نویسندگان
چکیده
منابع مشابه
Free Energy Landscapes of Vesicle Fusion by Umbrella Sampling MD Simulations
bilayer as two abutted monolayers, each with a neutral surface. The constraint imposed by mathematically placing two monolayers in apposition causes minimal energy to be larger than that predicated by (incorrectly) assuming that the elastic properties of a bilayer can be quantitatively captured through a single surface. Independent of pore size, the deformation of tilt did not appreciably affec...
متن کاملEfficient Determination of Free Energy Landscapes in Multiple Dimensions from Biased Umbrella Sampling Simulations Using Linear Regression
The weighted histogram analysis method (WHAM) is a standard protocol for postprocessing the information from biased umbrella sampling simulations to construct the potential of mean force with respect to a set of order parameters. By virtue of the WHAM equations, the unbiased density of state is determined by satisfying a self-consistent condition through an iterative procedure. While the method...
متن کاملAutomated Exploration of Free Energy Landscapes Based on Umbrella Integration.
We present a new approach for automated exploration of free energy landscapes on the basis of the umbrella integration (UI) method. The method to search points in the landscape relies on the normal distributions and gradients of the potential of mean force (PMF) obtained from UI calculations. We applied this approach to the alanine dipeptide in solution and demonstrated that the equilibrium and...
متن کاملSampling free energy surfaces as slices by combining umbrella sampling and metadynamics
Metadynamics (MTD) is a very powerful technique to sample high-dimensional free energy landscapes, and due to its self-guiding property, the method has been successful in studying complex reactions and conformational changes. MTD sampling is based on filling the free energy basins by biasing potentials and thus for cases with flat, broad, and unbound free energy wells, the computational time to...
متن کاملUmbrella sampling in non-equilibrium computer simulations
We describe the application of the umbrella sampling technique well known from equilibrium Monte Carlo to dynamical, non-equilibrium simulations. This method is used specifically to calculate the nucleation barrier of Brownian Yukawa particles in a homogeneous shear flow. 2005 Elsevier B.V. All rights reserved. PACS: 82.70.Dd; 61.20.Ja; 81.10.Aj; 83.60.Rs
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: Biophysical Journal
سال: 2013
ISSN: 0006-3495
DOI: 10.1016/j.bpj.2012.11.548