Literature DB >> 15268122

Calculation of free energy through successive umbrella sampling.

Peter Virnau1, Marcus Muller.   

Abstract

We consider an implementation of umbrella sampling in which the pertinent range of states is subdivided into small windows that are sampled consecutively and linked together. This allows us to simulate without a weight function or to extrapolate the results to the neighboring window in order to estimate a weight function. Additionally, we present a detailed error analysis in which we demonstrate that the error in umbrella sampling is controlled and, in the absence of sampling difficulties, independent of the window sizes. In this case, the efficiency of our implementation is comparable to a multicanonical simulation with a very good weight function, which in our scheme does not need to be known ahead of time. The analysis also allows us to detect sampling difficulties such as correlations between adjacent windows and provides a test of equilibration. We exemplify the scheme by simulating the liquid-vapor coexistence in a Lennard-Jones system.

Year:  2004        PMID: 15268122     DOI: 10.1063/1.1739216

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  14 in total

1.  New insights into human farnesyl pyrophosphate synthase inhibition by second-generation bisphosphonate drugs.

Authors:  D Fernández; R Ramis; J Ortega-Castro; R Casasnovas; B Vilanova; J Frau
Journal:  J Comput Aided Mol Des       Date:  2017-06-19       Impact factor: 3.686

2.  Toward the observation of a liquid-liquid phase transition in patchy origami tetrahedra: a numerical study.

Authors:  Simone Ciarella; Oleg Gang; Francesco Sciortino
Journal:  Eur Phys J E Soft Matter       Date:  2016-12-27       Impact factor: 1.890

3.  Eigenvector method for umbrella sampling enables error analysis.

Authors:  Erik H Thiede; Brian Van Koten; Jonathan Weare; Aaron R Dinner
Journal:  J Chem Phys       Date:  2016-08-28       Impact factor: 3.488

4.  Probing the wild-type HRas activation mechanism using steered molecular dynamics, understanding the energy barrier and role of water in the activation.

Authors:  Neeru Sharma; Uddhavesh Sonavane; Rajendra Joshi
Journal:  Eur Biophys J       Date:  2014-01-20       Impact factor: 1.733

5.  How to simulate patchy particles.

Authors:  Lorenzo Rovigatti; John Russo; Flavio Romano
Journal:  Eur Phys J E Soft Matter       Date:  2018-05-14       Impact factor: 1.890

6.  Mg2+ Impacts the Twister Ribozyme through Push-Pull Stabilization of Nonsequential Phosphate Pairs.

Authors:  Abhishek A Kognole; Alexander D MacKerell
Journal:  Biophys J       Date:  2020-01-28       Impact factor: 4.033

7.  On the existence of thermodynamically stable rigid solids.

Authors:  Parswa Nath; Saswati Ganguly; Jürgen Horbach; Peter Sollich; Smarajit Karmakar; Surajit Sengupta
Journal:  Proc Natl Acad Sci U S A       Date:  2018-04-19       Impact factor: 11.205

8.  A dynamic structural model of expanded RNA CAG repeats: a refined X-ray structure and computational investigations using molecular dynamics and umbrella sampling simulations.

Authors:  Ilyas Yildirim; HaJeung Park; Matthew D Disney; George C Schatz
Journal:  J Am Chem Soc       Date:  2013-02-26       Impact factor: 15.419

9.  Predicting Partition Coefficients of Neutral and Charged Solutes in the Mixed SLES-Fatty Acid Micellar System.

Authors:  Mattia Turchi; Abhishek A Kognole; Anmol Kumar; Qiong Cai; Guoping Lian; Alexander D MacKerell
Journal:  J Phys Chem B       Date:  2020-02-25       Impact factor: 2.991

10.  Parallel Prefetching for Canonical Ensemble Monte Carlo Simulations.

Authors:  Harold W Hatch
Journal:  J Phys Chem A       Date:  2020-08-25       Impact factor: 2.781

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