Literature DB >> 18282026

An integrate-over-temperature approach for enhanced sampling.

Yi Qin Gao1.   

Abstract

A simple method is introduced to achieve efficient random walking in the energy space in molecular dynamics simulations which thus enhances the sampling over a large energy range. The approach is closely related to multicanonical and replica exchange simulation methods in that it allows configurations of the system to be sampled in a wide energy range by making use of Boltzmann distribution functions at multiple temperatures. A biased potential is quickly generated using this method and is then used in accelerated molecular dynamics simulations.

Year:  2008        PMID: 18282026     DOI: 10.1063/1.2825614

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


  14 in total

1.  Enhanced sampling and applications in protein folding in explicit solvent.

Authors:  Cheng Zhang; Jianpeng Ma
Journal:  J Chem Phys       Date:  2010-06-28       Impact factor: 3.488

2.  Cy3-DNA stacking interactions strongly depend on the identity of the terminal basepair.

Authors:  Justin Spiriti; Jennifer K Binder; Marcia Levitus; Arjan van der Vaart
Journal:  Biophys J       Date:  2011-02-16       Impact factor: 4.033

3.  Molecular Dynamics Simulations with Quantum Mechanics/Molecular Mechanics and Adaptive Neural Networks.

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Journal:  J Chem Theory Comput       Date:  2018-02-26       Impact factor: 6.006

4.  A Study of Ion-Neutral Collision Cross Section Values for Low Charge States of Peptides, Proteins, and Peptide/Protein Complexes.

Authors:  Francisco A Fernandez-Lima; Ryan C Blase; David H Russell
Journal:  Int J Mass Spectrom       Date:  2010-12-01       Impact factor: 1.986

5.  QM/MM free energy simulations: recent progress and challenges.

Authors:  Xiya Lu; Dong Fang; Shingo Ito; Yuko Okamoto; Victor Ovchinnikov; Qiang Cui
Journal:  Mol Simul       Date:  2016-07-05       Impact factor: 2.178

6.  Trends in template/fragment-free protein structure prediction.

Authors:  Yaoqi Zhou; Yong Duan; Yuedong Yang; Eshel Faraggi; Hongxing Lei
Journal:  Theor Chem Acc       Date:  2010-09-01       Impact factor: 1.702

7.  How quickly can a β-hairpin fold from its transition state?

Authors:  Beatrice N Markiewicz; Lijiang Yang; Robert M Culik; Yi Qin Gao; Feng Gai
Journal:  J Phys Chem B       Date:  2014-03-17       Impact factor: 2.991

8.  Molecular simulation of water and hydration effects in different environments: challenges and developments for DFTB based models.

Authors:  Puja Goyal; Hu-Jun Qian; Stephan Irle; Xiya Lu; Daniel Roston; Toshifumi Mori; Marcus Elstner; Qiang Cui
Journal:  J Phys Chem B       Date:  2014-09-16       Impact factor: 2.991

9.  Rich Dynamics Underlying Solution Reactions Revealed by Sampling and Data Mining of Reactive Trajectories.

Authors:  Jun Zhang; Zhen Zhang; Yi Isaac Yang; Sirui Liu; Lijiang Yang; Yi Qin Gao
Journal:  ACS Cent Sci       Date:  2017-04-15       Impact factor: 14.553

10.  OpenPathSampling: A Python Framework for Path Sampling Simulations. 2. Building and Customizing Path Ensembles and Sample Schemes.

Authors:  David W H Swenson; Jan-Hendrik Prinz; Frank Noe; John D Chodera; Peter G Bolhuis
Journal:  J Chem Theory Comput       Date:  2018-12-31       Impact factor: 6.006

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