Found 34 Documents (Results 1–34)
Unraveling the complexity of Exendin-4 folding through two distinct pathways. (English) Zbl 1531.92034
Random batch sum-of-Gaussians method for molecular dynamics simulations of particle systems. (English) Zbl 07749373
Breaking down the parallel performance of GROMACS, a high-performance molecular dynamics software. (English) Zbl 1533.65008
Wyrzykowski, Roman (ed.) et al., Parallel processing and applied mathematics. 14th international conference, PPAM 2022, Gdansk, Poland, September 11–14, 2022. Revised selected papers. Part I. Cham: Springer. Lect. Notes Comput. Sci. 13826, 333-345 (2023).
A critical review on molecular dynamics applied to structure fracture and failure analysis. (English) Zbl 1511.74016
Multiscale hybrid modeling of proteins in solvent: SARS-CoV2 spike protein as test case for lattice Boltzmann – all atom molecular dynamics coupling. (English) Zbl 1508.92084
A scalable algorithm for many-body dissipative particle dynamics using multiple general purpose graphic processing units. (English) Zbl 07682147
High-performance large-scale atomistic simulation of thin films deposition. (English) Zbl 1502.82024
GROMACS implementation of free energy calculations with non-pairwise variationally derived intermediates. (English) Zbl 1539.82409
Molecular dynamics simulation of heat transfer and stresses in thin films caused by a short laser pulse. (English) Zbl 1479.82122
A generalized Newton iteration for computing the solution of the inverse Henderson problem. (English) Zbl 1461.65109
Task-based parallel computation of the density matrix in quantum-based molecular dynamics using graph partitioning. (English) Zbl 1383.82005
Reviewer: Vicenţiu D. Rădulescu (Craiova)
Efficient implementation of the many-body reactive bond order (REBO) potential on GPU. (English) Zbl 1349.82031
\(\Pi\)4U: a high performance computing framework for Bayesian uncertainty quantification of complex models. (English) Zbl 1352.65009
Wavelets as basis functions to represent the coarse-graining potential in multiscale coarse graining approach. (English) Zbl 1349.65736
MSC:
65T60
82C80
Molecular dynamics. With deterministic and stochastic numerical methods. (English) Zbl 1351.82001
Interdisciplinary Applied Mathematics 39. Cham: Springer (ISBN 978-3-319-16374-1/hbk; 978-3-319-16375-8/ebook). xxii, 443 p. (2015).
Reviewer: Georg Hebermehl (Berlin)
Automated parameterization of intermolecular pair potentials using global optimization techniques. (English) Zbl 1360.65174
A meshless discretization method for Markov state models applied to explicit water peptide folding simulations. (English) Zbl 1269.82072
Griebel, Michael (ed.) et al., Meshfree methods for partial differential equations VI. Selected papers of the sixth international workshop, Bonn, Germany, October 4–6, 2011. Berlin: Springer (ISBN 978-3-642-32978-4/hbk; 978-3-642-32979-1/ebook). Lecture Notes in Computational Science and Engineering 89, 141-154 (2013).
ESPResSO 3.1: molecular dynamics software for coarse-grained models. (English) Zbl 1269.82007
Griebel, Michael (ed.) et al., Meshfree methods for partial differential equations VI. Selected papers of the sixth international workshop, Bonn, Germany, October 4–6, 2011. Berlin: Springer (ISBN 978-3-642-32978-4/hbk; 978-3-642-32979-1/ebook). Lecture Notes in Computational Science and Engineering 89, 1-23 (2013).
Combining stochastic and deterministic approaches within high efficiency molecular simulations. (English) Zbl 1264.82077
A short note on the fast evaluation of dihedral angle potentials and their derivatives. (English) Zbl 1245.82002
MSC:
82-08
Orientations of special water dipoles that accelerate water molecules exiting from carbon nanotube. (English) Zbl 1238.81190
Implementing molecular dynamics on hybrid high performance computers-short range forces. (English) Zbl 1221.82008
Nose-Hoover thermostat length effect on thermal conductivity of single wall carbon nanotubes. (English) Zbl 1202.82100
MSC:
82D80
80A20
General purpose molecular dynamics simulations fully implemented on graphics processing units. (English) Zbl 1148.81301
An ergodic sampling scheme for constrained Hamiltonian systems with applications to molecular dynamics. (English) Zbl 1214.82063
MSC:
82C21
Simulating the physical world. Hierarchical modeling from quantum mechanics to fluid dynamics. (English) Zbl 1134.00009
Cambridge: Cambridge University Press (ISBN 978-0-521-83527-5/hbk). xxvii, 596 p. (2007).
Reviewer: Claudia-Veronika Meister (Potsdam)
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