Optimization of partial multicanonical molecular dynamics simulations applied to an alaninedipeptide in explicit water solvent

2011 ◽  
Vol 13 (1) ◽  
pp. 114-126 ◽  
Author(s):  
Hisashi Okumura
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Water Solvent ◽  
Dynamics Simulations ◽  
Explicit Water

scholarly journals Implicit Solvation Parameters Derived from Explicit Water Forces in Large-Scale Molecular Dynamics Simulations

2012 ◽  
Vol 8 (7) ◽  
pp. 2391-2403 ◽  
Author(s):  
Jens Kleinjung ◽  
Walter R. P. Scott ◽  
Jane R. Allison ◽  
Wilfred F. van Gunsteren ◽  
Franca Fraternali
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Large Scale ◽  
Implicit Solvation ◽  
Solvation Parameters ◽  
Dynamics Simulations ◽  
Explicit Water

Conformational analysis of compstatin analogues with molecular dynamics simulations in explicit water

2007 ◽  
Vol 26 (2) ◽  
pp. 571-580 ◽  
Author(s):  
Phanourios Tamamis ◽  
Spiros S. Skourtis ◽  
Dimitrios Morikis ◽  
John D. Lambris ◽  
Georgios Archontis
Keyword(s):  
Molecular Dynamics ◽  
Conformational Analysis ◽  
Molecular Dynamics Simulations ◽  
Dynamics Simulations ◽  
Explicit Water

Conformational analysis of compstatin analogues with molecular dynamics simulations in explicit water

2007 ◽  
Vol 44 (1-3) ◽  
pp. 150
Author(s):  
Georgios Archontis ◽  
Phanourios Tamamis ◽  
Spiros S. Skourtis ◽  
Dimitrios Morikis ◽  
John D. Lambris
Keyword(s):  
Molecular Dynamics ◽  
Conformational Analysis ◽  
Molecular Dynamics Simulations ◽  
Dynamics Simulations ◽  
Explicit Water

scholarly journals A molecular dynamics simulation study on the propensity of Asn-Gly-containing heptapeptides towards β-turn structures: Comparison with ab initio quantum mechanical calculations

PLoS ONE ◽  
2020 ◽  
Vol 15 (12) ◽  
pp. e0243429
Author(s):  
Dimitrios A. Mitsikas ◽  
Nicholas M. Glykos
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Molecular Dynamics Simulations ◽  
Dynamics Simulation ◽  
Quantum Mechanical ◽  
Type I ◽  
Quantum Mechanical Calculations ◽  
Water Solvent ◽  
Simulation Protocol ◽  
Dynamics Simulations

Both molecular mechanical and quantum mechanical calculations play an important role in describing the behavior and structure of molecules. In this work, we compare for the same peptide systems the results obtained from folding molecular dynamics simulations with previously reported results from quantum mechanical calculations. More specifically, three molecular dynamics simulations of 5 μs each in explicit water solvent were carried out for three Asn-Gly-containing heptapeptides, in order to study their folding and dynamics. Previous data, based on quantum mechanical calculations within the DFT framework have shown that these peptides adopt β-turn structures in aqueous solution, with type I’ β-turn being the most preferred motif. The results from our analyses indicate that at least for the given systems, force field and simulation protocol, the two methods diverge in their predictions. The possibility of a force field-dependent deficiency is examined as a possible source of the observed discrepancy.

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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