Exploration of conformational phase space in polymer melts: A comparison of parallel tempering and conventional molecular dynamics simulations

2001 ◽  
Vol 115 (3) ◽  
pp. 1121-1124 ◽  
Author(s):  
Dmitry Bedrov ◽  
Grant D. Smith
Keyword(s):  
Molecular Dynamics ◽  
Phase Space ◽  
Molecular Dynamics Simulations ◽  
Polymer Melts ◽  
Parallel Tempering ◽  
Dynamics Simulations

scholarly journals Polymer conformations in polymer nanocomposites containing spherical nanoparticles

Soft Matter ◽  
2015 ◽  
Vol 11 (2) ◽  
pp. 382-388 ◽  
Author(s):  
Argyrios Karatrantos ◽  
Nigel Clarke ◽  
Russell J. Composto ◽  
Karen I. Winey
Keyword(s):  
Molecular Dynamics ◽  
Percolation Threshold ◽  
Molecular Dynamics Simulations ◽  
Polymer Nanocomposites ◽  
Polymer Melts ◽  
Spherical Nanoparticles ◽  
Dynamics Simulations

We investigate the effect of various spherical nanoparticles on chain dimensions in polymer melts for high nanoparticle loading which is larger than the percolation threshold, using molecular dynamics simulations.

scholarly journals Isostaticity and the solidification of semiflexible polymer melts

Soft Matter ◽  
2017 ◽  
Vol 13 (43) ◽  
pp. 7948-7952 ◽  
Author(s):  
Christian O. Plaza-Rivera ◽  
Hong T. Nguyen ◽  
Robert S. Hoy
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Polymer Melts ◽  
Polymer Model ◽  
Soft Sphere ◽  
Semiflexible Polymer ◽  
Dynamics Simulations

Using molecular dynamics simulations of a tangent-soft-sphere bead-spring polymer model, we examine the degree to which semiflexible polymer melts solidify at isostaticity.

scholarly journals Combining enhanced sampling with experiment-directed simulation of the GYG peptide

2018 ◽  
Vol 17 (03) ◽  
pp. 1840007 ◽  
Author(s):  
Dilnoza B. Amirkulova ◽  
Andrew D. White
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Chemical Shifts ◽  
Parallel Tempering ◽  
Collective Variables ◽  
Novel Approach ◽  
Sampling Problem ◽  
Combination Of Methods ◽  
Dynamics Simulations ◽  
Explicit Water

Experiment-directed simulation (EDS) is a technique to minimally bias molecular dynamics simulations to match experimentally observed results. The method improves accuracy but does not address the sampling problem of molecular dynamics simulations of large systems. This work combines EDS with both the parallel-tempering or parallel-tempering well-tempered ensemble replica-exchange methods to enhance sampling. These methods are demonstrated on the GYG tripeptide in explicit water. The collective variables biased by EDS are chemical shifts, where the set-points are determined by NMR experiments. The results show that it is possible to enhance sampling with either parallel-tempering and parallel-tempering well-tempered ensemble in the EDS method. This combination of methods provides a novel approach for both accurately and exhaustively simulating biological systems.

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