Literature DB >> 23425452

Communication: Simulated tempering with fast on-the-fly weight determination.

Phuong H Nguyen1, Yuko Okamoto, Philippe Derreumaux.   

Abstract

We propose an efficient method to enhance sampling in computer simulations by combining the simulated tempering algorithm with a fast on-the-fly weight determination scheme. The weights are self-updated via a trapezoid rule during the simulated tempering simulation. With our proposed scheme, simulated tempering requires neither prior trial simulations nor complicated update schemes. The advantage of our method over replica exchange molecular dynamics has been demonstrated with the study of the folding of the 20-residue alanine peptide and the aggregation of a trimer formed by the Alzheimer's peptide fragment Aβ(16-22).

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Year:  2013        PMID: 23425452     DOI: 10.1063/1.4792046

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


  15 in total

1.  Locally weighted histogram analysis and stochastic solution for large-scale multi-state free energy estimation.

Authors:  Zhiqiang Tan; Junchao Xia; Bin W Zhang; Ronald M Levy
Journal:  J Chem Phys       Date:  2016-01-21       Impact factor: 3.488

2.  Effect of the Tottori familial disease mutation (D7N) on the monomers and dimers of Aβ40 and Aβ42.

Authors:  Man Hoang Viet; Phuong H Nguyen; Son Tung Ngo; Mai Suan Li; Philippe Derreumaux
Journal:  ACS Chem Neurosci       Date:  2013-09-16       Impact factor: 4.418

Review 3.  Amyloid β Protein and Alzheimer's Disease: When Computer Simulations Complement Experimental Studies.

Authors:  Jessica Nasica-Labouze; Phuong H Nguyen; Fabio Sterpone; Olivia Berthoumieu; Nicolae-Viorel Buchete; Sébastien Coté; Alfonso De Simone; Andrew J Doig; Peter Faller; Angel Garcia; Alessandro Laio; Mai Suan Li; Simone Melchionna; Normand Mousseau; Yuguang Mu; Anant Paravastu; Samuela Pasquali; David J Rosenman; Birgit Strodel; Bogdan Tarus; John H Viles; Tong Zhang; Chunyu Wang; Philippe Derreumaux
Journal:  Chem Rev       Date:  2015-03-19       Impact factor: 60.622

4.  Coarse-grained dynamic RNA titration simulations.

Authors:  S Pasquali; E Frezza; F L Barroso da Silva
Journal:  Interface Focus       Date:  2019-04-19       Impact factor: 3.906

Review 5.  Molecular simulations by generalized-ensemble algorithms in isothermal-isobaric ensemble.

Authors:  Masataka Yamauchi; Yoshiharu Mori; Hisashi Okumura
Journal:  Biophys Rev       Date:  2019-05-21

6.  Optimal updating magnitude in adaptive flat-distribution sampling.

Authors:  Cheng Zhang; Justin A Drake; Jianpeng Ma; B Montgomery Pettitt
Journal:  J Chem Phys       Date:  2017-11-07       Impact factor: 3.488

7.  What Can Human-Guided Simulations Bring to RNA Folding?

Authors:  Liuba Mazzanti; Sébastien Doutreligne; Cedric Gageat; Philippe Derreumaux; Antoine Taly; Marc Baaden; Samuela Pasquali
Journal:  Biophys J       Date:  2017-06-22       Impact factor: 4.033

8.  Effects of Zn2+ binding on the structural and dynamic properties of amyloid β peptide associated with Alzheimer's disease: Asp1 or Glu11?

Authors:  Liang Xu; Xiaojuan Wang; Xicheng Wang
Journal:  ACS Chem Neurosci       Date:  2013-09-13       Impact factor: 4.418

Review 9.  The OPEP protein model: from single molecules, amyloid formation, crowding and hydrodynamics to DNA/RNA systems.

Authors:  Fabio Sterpone; Simone Melchionna; Pierre Tuffery; Samuela Pasquali; Normand Mousseau; Tristan Cragnolini; Yassmine Chebaro; Jean-Francois St-Pierre; Maria Kalimeri; Alessandro Barducci; Yoann Laurin; Alex Tek; Marc Baaden; Phuong Hoang Nguyen; Philippe Derreumaux
Journal:  Chem Soc Rev       Date:  2014-04-23       Impact factor: 54.564

10.  Protein Simulations in Fluids: Coupling the OPEP Coarse-Grained Force Field with Hydrodynamics.

Authors:  Fabio Sterpone; Philippe Derreumaux; Simone Melchionna
Journal:  J Chem Theory Comput       Date:  2015-04-14       Impact factor: 6.006

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