Umbrella sampling in non-equilibrium computer simulations
نویسندگان
چکیده
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
منابع مشابه
CTMS Fellowship Report
In the studies of force-induced conformational transitions of biomolecules, the large time-scale difference from experiments presents the challenge of obtaining convergent sampling for molecular dynamics simulations. To circumvent this fundamental problem, an approach combining the replica-exchange method and umbrella sampling (REM-US) is developed to simulate mechanical stretching of polysacch...
متن کاملUmbrella sampling for nonequilibrium processes.
The authors introduce an algorithm for determining the steady-state probability distribution of an ergodic system arbitrarily far from equilibrium. By enforcing equal sampling of different regions of phase space, as in umbrella sampling simulations of systems at equilibrium, low probability regions are explored to a much greater extent than in physically weighted simulations. The algorithm can ...
متن کاملMultidimensional adaptive umbrella sampling: Applications to main chain and side chain peptide conformations
A new adaptive umbrella sampling technique for molecular dynamics simulations is described. The high efficiency of the technique renders multidimensional adaptive umbrella sampling possible and thereby enables uniform sampling of the conformational space spanned by several degrees of freedom. The efficiency is achieved by using the weighted histogram analysis method to combine the results from ...
متن کاملFinite representation of an infinite bulk system: Solvent boundary potential for computer simulations
An approach is developed to obtain statistical properties similar to those of an infinite bulk system from computer simulations of a finite cluster. A rigorous theoretical formulation is given for the solvent boundary potential which takes the influence of the surrounding bulk into account. The solvent boundary potential is the configuration-dependent solvation free energy of an effective clust...
متن کاملThermodynamics of Protein Folding Studied by Umbrella Sampling along a Reaction Coordinate of Native Contacts.
Spontaneous transitions between the native and non-native protein conformations are normally rare events that hardly take place in typical unbiased molecular dynamics simulations. It was recently demonstrated that such transitions can be well described by a reaction coordinate, Q, that represents the collective fraction of the native contacts between the protein atoms. Here we attempt to use th...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
برای دانلود متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید
ثبت ناماگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید
ورودعنوان ژورنال:
- Computer Physics Communications
دوره 169 شماره
صفحات -
تاریخ انتشار 2005