Literature DB >> 26178083

Communication: Multiple atomistic force fields in a single enhanced sampling simulation.

Man Hoang Viet1, Philippe Derreumaux2, Phuong H Nguyen2.   

Abstract

The main concerns of biomolecular dynamics simulations are the convergence of the conformational sampling and the dependence of the results on the force fields. While the first issue can be addressed by employing enhanced sampling techniques such as simulated tempering or replica exchange molecular dynamics, repeating these simulations with different force fields is very time consuming. Here, we propose an automatic method that includes different force fields into a single advanced sampling simulation. Conformational sampling using three all-atom force fields is enhanced by simulated tempering and by formulating the weight parameters of the simulated tempering method in terms of the energy fluctuations, the system is able to perform random walk in both temperature and force field spaces. The method is first demonstrated on a 1D system and then validated by the folding of the 10-residue chignolin peptide in explicit water.

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Year:  2015        PMID: 26178083     DOI: 10.1063/1.4926535

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


  2 in total

1.  Conformational Ensembles of the Wild-Type and S8C Aβ1-42 Dimers.

Authors:  Viet Hoang Man; Phuong H Nguyen; Philippe Derreumaux
Journal:  J Phys Chem B       Date:  2017-03-10       Impact factor: 2.991

2.  In silico structural characterization of protein targets for drug development against Trypanosoma cruzi.

Authors:  Carlyle Ribeiro Lima; Nicolas Carels; Ana Carolina Ramos Guimaraes; Pierre Tufféry; Philippe Derreumaux
Journal:  J Mol Model       Date:  2016-09-24       Impact factor: 1.810

  2 in total

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