R. Abagyan, M. Totrov, and D. Kuznetsov, Icm-a new method for protein modeling and design: applications to docking and structure prediction from the distorted native conformation, Journal of computational chemistry, vol.15, issue.5, p.20, 1994.

S. Aboud, M. Marreiro, R. Saraniti, and . Eisenberg, A poisson p 3 m force field scheme for particle-based simulations of ionic liquids, Journal of Computational Electronics, vol.3, issue.2, p.27, 2004.

E. Agullo, B. Bramas, O. Coulaud, E. Darve, M. Messner et al., Task-based fmm for multicore architectures, SIAM Journal on Scientific Computing, vol.36, issue.1, p.27, 2014.
URL : https://hal.archives-ouvertes.fr/hal-00807368

A. Aksimentiev, Deciphering ionic current signatures of dna transport through a nanopore, Nanoscale, vol.2, issue.4, p.126, 2010.

A. Aksimentiev, B. Jiunn, G. Heng, K. Timp, and . Schulten, Microscopic kinetics of dna translocation through synthetic nanopores, Biophysical journal, vol.87, issue.3, p.126, 2004.

D. J. Michael-p-allen and . Tildesley, Computer simulation of liquids, p.61, 2017.

A. Amadei, A. Linssen, J. C. Herman, and . Berendsen, Essential dynamics of proteins, Proteins: Structure, Function, and Bioinformatics, vol.17, issue.4, p.149, 1993.

U. Ananthakrishnaiah, R. P. Manohar, and J. Stephenson, Fourth-order finite difference methods for three-dimensional general linear elliptic problems with variable coefficients, Numerical Methods for Partial Differential Equations, vol.3, issue.3, pp.229-240, 1987.
DOI : 10.1002/num.1690030307

K. Andrey and K. Anatoly, Formation of the large-scale structure in the universe: filaments, 2018.

A. Arnold, F. Fahrenberger, C. Holm, O. Lenz, M. Bolten et al., Comparison of scalable fast methods for long-range interactions, Physical Review E-Statistical, Nonlinear, and Soft Matter Physics, vol.88, issue.6, p.63308, 2013.

, Vladimir Igorevich Arnol'd. Mathematical methods of classical mechanics, vol.60, 2013.

S. Artemova, Adaptive algorithms for molecular simulation, p.33, 2012.
URL : https://hal.archives-ouvertes.fr/tel-00846690

S. Artemova and S. Redon, Adaptively restrained particle simulations, Physical Review Letters, vol.109, issue.19, p.190201, 2012.
DOI : 10.1103/physrevlett.109.190201
URL : https://hal.archives-ouvertes.fr/hal-00756121

D. Stanislav-m-avdoshenko, C. Nozaki, . Gomes-da-rocha, W. Jhon, . Gonzalez et al., Dynamic and electronic transport properties of dna translocation through graphene nanopores, Nano letters, vol.13, issue.5, p.130, 2013.

P. Balbuena and J. M. Seminario, Molecular dynamics: from classical to quantum methods, vol.7, 1999.

V. Ballenegger, J. J. Cerda, O. Lenz, and C. Holm, The optimal P3M algorithm for computing electrostatic energies in periodic systems, Journal of Chemical Physics, vol.128, issue.3, p.27, 2008.
URL : https://hal.archives-ouvertes.fr/hal-00276427

V. Ballenegger, J. J. Cerdà, and C. Holm, Removal of spurious self-interactions in particle-mesh methods, Computer Physics Communications, vol.182, issue.9, pp.1919-1923, 2011.
URL : https://hal.archives-ouvertes.fr/hal-00653454

J. C. Herman, . Berendsen, P. M. James, W. F. Postma, J. Van-gunsteren et al., Interaction models for water in relation to protein hydration, Intermolecular forces, p.22, 1981.

J. C. Herman, D. Berendsen, . Van-der, R. Spoel, and . Van-drunen, Gromacs: a message-passing parallel molecular dynamics implementation, Computer Physics Communications, vol.91, issue.1-3, pp.43-56, 1995.

. Hjc-berendsen, T. P. Grigera, and . Straatsma, The missing term in effective pair potentials, Journal of Physical Chemistry, vol.91, issue.24, p.22, 1987.

M. Bruce-j-berne, J. E. Borkovec, and . Straub, Classical and modern methods in reaction rate theory, The Journal of Physical Chemistry, vol.92, issue.13, p.15, 1988.

M. Sergey, I. Bezrukov, . Vodyanoy, and . Parsegian, Counting polymers moving through a single ion channel, Nature, vol.370, issue.6487, p.126, 1994.

.. A. Bhattacharya and . Bhattacharya, wh morrison, k. luo, t. ala-nissila, sc ying, a. milchev, and k. binder, eur. phys, Eur. Phys. J. E, vol.29, p.128, 2009.

L. Bluestein, A linear filtering approach to the computation of discrete fourier transform, IEEE Transactions on Audio and Electroacoustics, vol.18, issue.4, p.46, 1970.

M. Bolten, Multigrid methods for structured grids and their application in particle simulation, 2008.

N. Bou-rabee, Time integrators for molecular dynamics, Entropy, vol.16, issue.1, p.19, 2013.

R. Bracewell, The Fourier transform and its applications, vol.31999, p.45, 1986.

R. E. James-h-bramble, J. E. Ewing, J. Pasciak, ;. Shen, J. Brandt et al., The analysis of multigrid algorithms for cell centered finite difference methods, Advances in Computational Mathematics, vol.5, issue.1, p.49, 1996.

A. Brandt and O. E. Livne, Multigrid Techniques : 1984 Guide With Applications to Fluid Dynamics, Classics in Applied Mathematics. Society for Industrial and Applied Mathematics, 2008.

D. Branton, W. David, A. Deamer, H. Marziali, . Bayley et al.,

. Huang, The potential and challenges of nanopore sequencing, Nature biotechnology, vol.26, issue.10, p.126, 2008.

W. Donald and . Brenner, Empirical potential for hydrocarbons for use in simulating the chemical vapor deposition of diamond films, Physical review B, vol.42, issue.15, p.9458, 1990.

W. Briggs, S. Van-emden-henson, and . Mccormick, A Multigrid Tutorial, Society for Industrial and Applied Mathematics, vol.37, p.107, 2000.
DOI : 10.1137/1.9780898719505

E. Brigham, The fast Fourier transform and its applications, vol.1, p.45, 1988.

R. E. Bernard-r-brooks, . Bruccoleri, D. Barry, D. J. Olafson, . States et al., Charmm: a program for macromolecular energy, minimization, and dynamics calculations, Journal of computational chemistry, vol.4, issue.2, p.11, 1983.

A. Richard and . Buckingham, The classical equation of state of gaseous helium, neon and argon, Proc. R. Soc. Lond. A, vol.168, p.16, 1938.

E. Cances, M. Defranceschi, W. Kutzelnigg, C. L. Bris, and Y. Maday, Computational quantum chemistry: a primer. Handbook of numerical analysis, vol.10, pp.3-270, 2003.

S. David, D. Cerutti, and . Case, Multi-level ewald: A hybrid multigrid/fast fourier transform approach to the electrostatic particle-mesh problem, Journal of chemical theory and computation, vol.6, issue.2, pp.443-458, 2009.

A. Chandramowlishwaran, K. Madduri, and R. Vuduc, Diagnosis, tuning, and redesign for multicore performance: A case study of the fast multipole method, Proceedings of the 2010 ACM/IEEE International Conference for High Performance Computing, Networking, Storage and Analysis, p.27, 2010.

J. Chen, C. L. Brooks, I. , and J. Khandogin, Recent advances in implicit solvent-based methods for biomolecular simulations. Current opinion in structural biology, vol.18, p.22, 2008.
DOI : 10.1016/j.sbi.2008.01.003
URL : http://europepmc.org/articles/pmc2386893?pdf=render

R. Chin, F. A. Hedstrom, and . Howes, Considerations on solving problems with multiple scales, Multiple Time Scales, pp.1-27, 1985.

. John-d-chodera, C. William, F. Swope, J. Noé, . Prinz et al., Dynamical reweighting: Improved estimates of dynamical properties from simulations at multiple temperatures, The Journal of chemical physics, vol.134, issue.24, p.137, 2011.

E. Chow and R. Hu, A survey of parallelization techniques for multigrid. Parallel processing for scientific computing, vol.20, p.107, 2006.

. Charles-k-chui, Wavelets: a mathematical tool for signal analysis, vol.1, p.41, 1997.

. Charles-k-chui, An introduction to wavelets, 2016.

A. Cisneros, V. Babin, and C. Sagui, Electrostatics interactions in classical simulations, Biomolecular Simulations, pp.243-270
DOI : 10.1007/978-1-62703-017-5_10

. Springer, , p.27, 2013.

W. James, J. W. Cooley, and . Tukey, An algorithm for the machine calculation of complex fourier series, Mathematics of computation, vol.19, issue.90, p.46, 1965.

D. Wendy, P. Cornell, C. I. Cieplak, I. R. Bayly, K. M. Gould et al., A second generation force field for the simulation of proteins, BIBLIOGRAPHY nucleic acids, and organic molecules, Journal of the American Chemical Society, vol.117, issue.19, pp.5179-5197, 1995.

O. Coulaud, P. Fortin, and J. Roman, Hybrid mpi-thread parallelization of the fast multipole method, Parallel and Distributed Computing, 2007. ISPDC'07. Sixth International Symposium on, pp.52-52
URL : https://hal.archives-ouvertes.fr/inria-00131001

, IEEE, p.27, 2007.

O. Coulaud, P. Fortin, and J. Roman, High performance blas formulation of the adaptive fast multipole method, Mathematical and Computer Modelling, vol.51, issue.3-4, p.27, 2010.
URL : https://hal.archives-ouvertes.fr/hal-00301521

J. Christopher and . Cramer, Essentials of computational chemistry: theories and models, p.12, 2013.

D. Frenkel and B. Smit, Understanding Molecular Simulation: from Algorithms to Applications, p.61, 2002.

M. Deserno and C. Holm, How to mesh up {E}wald sums. 2. An accurate error estimate for the P3M algorithm, J. Chem. Phys, vol.109, p.7694, 1998.

M. Deserno and C. Holm, How to mesh up Ewald sums. I. a theoretical and numerical comparison of various particle mesh routines, Journal of Chemical Physics, vol.109, issue.18, p.61, 1998.

J. Dubbeldam, . Milchev, T. Vg-rostiashvili, and . Vilgis, Polymer translocation through a nanopore: A showcase of anomalous diffusion, Physical Review E, vol.76, issue.1, p.138, 2007.

J. Dubbeldam, A. Milchev, T. Vg-rostiashvili, and . Vilgis, Driven polymer translocation through a nanopore: A manifestation of anomalous diffusion

, Europhysics Letters), vol.79, issue.1, p.18002, 2007.

S. Prince, A. Edorh, and S. Redon, Incremental update of electrostatic interactions in adaptively restrained particle simulations, Journal of Computational Chemistry, vol.0, issue.0, p.35, 2018.

.. U. U-essmann and L. Pedersen, j. chem. phys, vol.103, p.8577, 1995.

U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee et al., A smooth particle mesh Ewald method, The Journal of Chemical Physics, vol.103, issue.19, pp.8577-8593, 1995.

F. Farahpour, A. Maleknejad, F. Varnik, and M. R. Ejtehadi, Chain deformation in translocation phenomena, Soft Matter, vol.9, issue.9, p.130, 2013.

R. W. Scott-e-feller, A. Pastor, S. Rojnuckarin, B. Bogusz, and . Brooks, Effect of electrostatic force truncation on interfacial and transport properties of water, The Journal of Physical Chemistry, vol.100, issue.42, pp.17011-17020, 1996.

J. Christopher, . Fennell, and . Gezelter, Is the ewald summation still necessary? pairwise alternatives to the accepted standard for long-range electrostatics, The Journal of chemical physics, vol.124, issue.23, p.28, 2006.

D. Fologea, E. Brandin, J. Uplinger, D. Branton, and J. Li, Dna conformation and base number simultaneously determined in a nanopore

, Electrophoresis, vol.28, issue.18, p.129, 2007.

. James-b-foresman, A. Todd, K. B. Keith, J. Wiberg, and . Snoonian,

J. Michael and . Frisch, Solvent effects. 5. influence of cavity shape, truncation of electrostatics, and electron correlation on ab initio reaction field calculations, The Journal of Physical Chemistry, vol.100, issue.40, pp.16098-16104, 1996.

E. Forest, Geometric integration for particle accelerators, Journal of Physics A: Mathematical and General, vol.39, issue.19, p.5321, 2006.

E. Forest and . Ronald-d-ruth, Fourth-order symplectic integration, Physica D: Nonlinear Phenomena, vol.43, issue.1, pp.105-117, 1990.

B. Fornberg, Generation of finite difference formulas on arbitrarily spaced grids, Mathematics of computation, vol.51, issue.184, p.112, 1988.

M. Frigo and . Steven-g-johnson, The design and implementation of fftw3, Proceedings of the IEEE, vol.93, p.46, 2005.

R. Fuentes, -. , and M. C. Barbosa, Sodium chloride, nacl/: New force field, The Journal of Physical Chemistry B, vol.120, issue.9, pp.2460-2470, 2016.

M. Fyta, Threading dna through nanopores for biosensing applications, Journal of physics: condensed Matter, vol.27, issue.27, p.126, 2015.

G. Michel, G. Gauthier, and . Slater, Nondriven polymer translocation through a nanopore: Computational evidence that the escape and relaxation processes are coupled, Physical Review E, vol.79, issue.2, p.128, 2009.

W. Gautschi, Numerical analysis, p.101, 2011.

A. M. Matthew-a-gebbie, . Smith, A. Howard, G. G. Dobbs, X. Warr et al., Long range electrostatic forces in ionic liquids, Chemical Communications, vol.53, issue.7, p.122, 2017.

C. Anna, P. Gilbert, M. Indyk, L. Iwen, and . Schmidt, Recent developments in the sparse fourier transform: A compressed fourier transform for big data, IEEE Signal Processing Magazine, vol.31, issue.5, p.76, 2014.

H. Goldstein, Classical mechanics. Pearson Education India, 2011.

T. Gradl, C. Freundl, H. Köstler, and U. Rüde, Scalable multigrid. High Performance Computing in Science and Engineering

/. Garching and . Munich, , p.49, 2007.

L. Greengard and V. Rokhlin, A fast algorithm for particle simulations, Journal of computational physics, vol.73, issue.2, p.27, 1987.

M. Griebel, S. Knapek, and G. Zumbusch, Numerical simulation in molecular dynamics. numerics, algorithms, parallelization, applications, volume 5 of texts in computational science and engineering, 2007.

H. Grubmüller, H. Heller, A. Windemuth, and K. Schulten, Generalized verlet algorithm for efficient molecular dynamics simulations with long-range interactions, Molecular Simulation, vol.6, issue.1-3, pp.121-142, 1991.

B. Guillot, A reappraisal of what we have learnt during three decades of computer simulations on water, Journal of Molecular Liquids, vol.101, issue.1-3, p.22, 2002.

P. Güntert, C. Mumenthaler, and K. Wüthrich, Torsion angle dynamics for nmr structure calculation with the new program dyana1, Journal of molecular biology, vol.273, issue.1, p.20, 1997.

W. Hackbusch, Multi-grid methods and applications, vol.4, p.96, 2013.

E. Hairer, C. Lubich, and G. Wanner, Geometric numerical integration: structure-preserving algorithms for ordinary differential equations, vol.31, 2006.

. Ulrich-he-hansmann, Parallel tempering algorithm for conformational studies of biological molecules, Chemical Physics Letters, vol.281, issue.1-3, p.137, 1997.

J. David, Z. Hardy, . Wu, C. James, J. E. Phillips et al., Multilevel Summation Method for Electrostatic Force Evaluation, Journal of Chemical Theory and Computation, vol.11, issue.2, pp.766-779, 2015.

J. David, . Hardy, A. Matthew, J. Wolff, K. Xia et al., Multilevel summation with b-spline interpolation for pairwise interactions in molecular dynamics simulations, The Journal of chemical physics, vol.144, issue.11, p.28, 2016.

H. Hassanieh, P. Indyk, D. Katabi, and E. Price, Simple and practical algorithm for sparse fourier transform, Proceedings of the twenty-third annual ACM-SIAM symposium on Discrete Algorithms, p.76, 2012.

P. W. Hemker, On the order of prolongations and restrictions in multigrid procedures, Journal of Computational and Applied Mathematics, vol.32, issue.3, p.127, 1990.

R. Hockney and J. Eastwood, Computer Simulation Using Particles, vol.25, 1988.
DOI : 10.1887/0852743920

C. Holm, Efficient methods for long range interactions in periodic geometries plus one application, Computational Soft Matter: From Synthetic Polymers to Proteins, vol.23, p.63, 2004.

G. William and . Hoover, Canonical dynamics: equilibrium phase-space distributions, Physical review A, vol.31, issue.3, p.1695, 1985.

L. Hörmander, Hypoelliptic second order differential equations, Acta Mathematica, vol.119, issue.1, pp.147-171, 1967.

P. Hsiao, Polyelectrolyte threading through a nanopore, Polymers, vol.8, issue.3, p.73, 2016.

G. Hu, M. Mao, and S. Ghosal, Ion transport through a graphene nanopore, Nanotechnology, vol.23, issue.39, p.110, 2012.

M. Hülsemann, F. Kowarschik, M. Mohr, and U. Rüde, Parallel Geometric Multigrid, p.107, 2006.

G. Nathan, F. E. Hunt, and . Cohen, Fast lookup tables for interatomic interactions, Journal of computational chemistry, vol.17, issue.16, p.25, 1996.

T. Ikonen and A. Bhattacharya, Tapio Ala-Nissila, and Wokyung Sung. Influence of pore friction on the universal aspects of driven polymer translocation

, Europhysics Letters), vol.103, issue.3, p.129, 2013.

. Illumina and . Illumina, , p.127, 2018.

A. Jain, G. Vaidehi, and . Rodriguez, A fast recursive algorithm for molecular dynamics simulation, Journal of Computational Physics, vol.106, issue.2, p.20, 1993.

F. Jensen, Introduction to computational chemistry, p.16, 2017.

L. William, J. D. Jorgensen, and . Madura, Quantum and statistical mechanical studies of liquids. 25. solvation and conformation of methanol in water, Journal of the American Chemical Society, vol.105, issue.6, p.22, 1983.

J. D. William-l-jorgensen, . Madura, and . Swenson, Optimized intermolecular potential functions for liquid hydrocarbons, Journal of the American Chemical Society, vol.106, issue.22, p.20, 1984.

K. A. Wetterstrand, Dna sequencing costs: Data from the nhgri genome sequencing program (gsp), 2018. URL www.genome.gov/sequencingcostsdata, p.127

K. Kadau, P. Timothy-c-germann, and . Lomdahl, Molecular dynamics comes of age: 320 billion atom simulation on bluegene/l, International Journal of Modern Physics C, vol.17, issue.12, pp.1755-1761, 2006.

P. Kar and M. Feig, Hybrid all-atom/coarse-grained simulations of proteins by direct coupling of charmm and primo force fields, Journal of chemical theory and computation, vol.13, issue.11, pp.5753-5765, 2017.

E. John-j-kasianowicz, D. Brandin, D. W. Branton, and . Deamer, Characterization of individual polynucleotide molecules using a membrane channel, Proceedings of the National Academy of Sciences, vol.93, issue.24, p.126, 1996.

J. John, J. Kasianowicz, E. R. Wf-robertson, J. E. Chan, V. Reiner et al., Nanoscopic porous sensors, Annu. Rev. Anal. Chem, vol.1, p.126, 2008.

W. H. Keesom, The second viral coefficient for rigid spherical molecules, whose mutual attraction is equivalent to that of a quadruplet placed at their centre, Proc

R. Acad and . Sci, , vol.18, p.15, 1915.

F. Ulrich and . Keyser, Controlling molecular transport through nanopores, Journal of The Royal Society Interface, p.128, 2011.

S. Kmiecik, D. Gront, M. Kolinski, L. Wieteska, A. E. Dawid et al., Coarse-grained protein models and their applications, Chemical Reviews, vol.116, issue.14, pp.7898-7936, 2016.

J. Kolafa and J. W. Perram, Cutoff errors in the Ewald summation formulae for point charge systems, Molecular Simulation, vol.9, issue.5, pp.351-368, 1992.

W. David-b-kony, S. Damm, W. F. Stoll, P. H. Van-gunsteren, and . Hünenberger, Explicit-solvent molecular dynamics simulations of the polysaccharide schizophyllan in water, Biophysical journal, vol.93, issue.2, pp.442-455, 2007.

M. Kowarschik and C. Weiss, Dimepack-a cache-optimized multigrid library, Proceedings of the International Conference on Parallel and Distributed Processing Techniques and Applications-VOLUME I. Citeseer, p.49, 2001.

R. Kubo, M. Toda, and N. Hashitsume, Statistical physics II: nonequilibrium statistical mechanics, vol.31, p.10, 2012.

M. Kuhlen, M. Vogelsberger, and R. Angulo, Numerical simulations of the dark universe: State of the art and the next decade, Physics of the Dark Universe, vol.1, issue.1-2, pp.50-93, 2012.

Y. Do and . Kwak, V-cycle multigrid for cell-centered finite differences, SIAM Journal on Scientific Computing, vol.21, issue.2, p.54, 1999.

, LAMMPS. Spc/e water system (4500 particles, p.68, 2017.

M. Levitt and A. Warshel, Computer simulation of protein folding, Nature, vol.253, issue.5494, p.20, 1975.

J. Li, Y. Zhang, J. Yang, K. Bi, Z. Ni et al., Molecular dynamics study of dna translocation through graphene nanopores, Physical Review E, vol.87, issue.6, p.130, 2013.

H. Lin and . Donald-g-truhlar, Qm/mm: what have we learned, where are we, and where do we go from here? Theoretical Chemistry Accounts, vol.117, p.20, 2007.

Z. Lin, E. Leveugle, E. M. Bringa, and L. V. Zhigilei, Molecular dynamics simulation of laser melting of nanocrystalline au, The Journal of Physical Chemistry C, vol.114, issue.12, pp.5686-5699, 2009.

Y. Daniel, X. Ling, and . Ling, On the distribution of dna translocation times in solid-state nanopores: an analysis using schrodinger s first-passage-time theory, Journal of Physics: Condensed Matter, vol.25, issue.37, p.375102, 2013.

H. Lodish, A. Berk, L. Zipursky, P. Matsudaira, D. Baltimore et al., Molecular cell biology, vol.3, 1995.

, Base4 Innovation Ltd, vol.4, p.127, 2018.

K. David, . Lubensky, and . David-r-nelson, Driven polymer translocation through a narrow pore, Biophysical Journal, vol.77, issue.4, pp.1824-1838, 1999.

J. Luo, L. Liu, P. Su, P. Duan, and D. Lu, A piecewise lookup table for calculating nonbonded pairwise atomic interactions, Journal of molecular modeling, vol.21, issue.11, p.25, 2015.

K. Luo, T. Ala-nissila, S. Ying, and A. Bhattacharya, Sequence dependence of dna translocation through a nanopore, Physical review letters, vol.100, issue.5, p.128, 2008.

K. Luo, T. T. Santtu, I. Ollila, T. Huopaniemi, P. Ala-nissila et al., Dynamical scaling exponents for polymer translocation through a nanopore, Physical Review E, vol.78, issue.5, p.50901, 2008.

B. Ma and R. Nussinov, Explicit and implicit water simulations of a ?-hairpin peptide, Proteins: Structure, Function, and Bioinformatics, vol.37, issue.1, p.22, 1999.

B. Alexander-d-mackerell, . Brooks, L. Charles, L. Brooks, B. Nilsson et al., Charmm: the energy function and its parameterization. Encyclopedia of computational chemistry, 1998.

A. Jr, D. Bashford, R. L. Bellott, J. D. Dunbrack, . Evanseck et al., All-atom empirical potential for molecular modeling and dynamics studies of proteins, The journal of physical chemistry B, vol.102, issue.18, p.13, 1998.

W. Michael and W. Mahoney, A five-site model for liquid water and the reproduction of the density anomaly by rigid, nonpolarizable potential functions, The Journal of Chemical Physics, vol.112, issue.20, p.22, 2000.

E. Marinari and G. Parisi, Simulated tempering: a new monte carlo scheme, Europhysics Letters), vol.19, issue.6, p.137, 1992.

P. Mark and L. Nilsson, Structure and dynamics of the tip3p, spc, and spc/e water models at 298 k, The Journal of Physical Chemistry A, vol.105, issue.43, p.130, 2001.

. Siewert-j-marrink, S. Jelger-risselada, . Yefimov, and . Peter-tieleman,

A. Vries, The martini force field: coarse grained model for biomolecular simulations. The journal of physical chemistry B, vol.111, p.20, 2007.

J. Mathé, A. Aksimentiev, K. David-r-nelson, A. Schulten, and . Meller, Orientation discrimination of single-stranded dna inside the ?-hemolysin membrane channel, Proceedings of the National Academy of Sciences of the United States of America, vol.102, p.130, 2005.

R. Mathias, S. Gabriel, and L. Tony, Free Energy Computations: A Mathematical Perspective, p.10, 2010.

. Stephen-l-mayo, W. Barry-d-olafson, and . Goddard, Dreiding: a generic force field for molecular simulations, Journal of Physical chemistry, vol.94, issue.26, p.13, 1990.

T. Menais, S. Mossa, and A. Buhot, Polymer translocation through nano-pores in vibrating thin membranes, Scientific reports, vol.6, p.38558, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01917228

R. Metzler and J. Klafter, When translocation dynamics becomes anomalous, Biophysical journal, vol.85, issue.4, p.136, 2003.
DOI : 10.1016/s0006-3495(03)74699-2
URL : https://doi.org/10.1016/s0006-3495(03)74699-2

A. Michels, H. Wijker, and H. K. Wijker, Isotherms of argon between 0 c and 150 c and pressures up to 2900 atmospheres, Physica, vol.15, issue.7, p.33, 1949.

A. Milchev, Single-polymer dynamics under constraints: scaling theory and computer experiment, Journal of Physics: Condensed Matter, vol.23, issue.10, p.103101, 2011.
DOI : 10.1088/0953-8984/23/10/103101

A. Milchev and K. Binder, Static and dynamic properties of adsorbed chains at surfaces: Monte carlo simulation of a bead-spring model, Macromolecules, vol.29, issue.1, p.130, 1996.

V. Gradimir, Z. Milovanovi´cmilovanovi´c, and . Udovi?i´udovi?i´c, Calculation of coefficients of a cardinal B-spline, Applied Mathematics Letters, vol.23, issue.11, pp.1346-1350, 2010.

A. Miotello and P. M. Ossi, Laser-surface interactions for new materials production, vol.130, 2010.

U. Mirsaidov, J. Comer, V. Dimitrov, A. Aksimentiev, and G. Timp, Slowing the translocation of double-stranded dna using a nanopore smaller than the double helix, Nanotechnology, vol.21, issue.39, p.126, 2010.

M. Mohr and R. Wienands, Cell-centred multigrid revisited, Computing and Visualization in Science, vol.7, issue.3, p.54, 2004.
DOI : 10.1007/s00791-004-0137-0

F. Molitor, J. Güttinger, C. Stampfer, D. Graf, T. Ihn et al., Local gating of a graphene hall bar by graphene side gates, Phys. Rev. B, vol.76, p.119, 2007.

F. Mondaini and . Moriconi, Markovian description of unbiased polymer translocation, Physics Letters A, vol.376, issue.45, p.128, 2012.

G. Stan, P. Moore, and . Crozier, Extension and evaluation of the multilevel summation method for fast long-range electrostatics calculations, The Journal of chemical physics, vol.140, issue.23, p.28, 2014.

M. Muthukumar, Polymer translocation through a hole, The Journal of Chemical Physics, vol.111, issue.22, pp.10371-10374, 1999.

I. Newton, The Principia: mathematical principles of natural philosophy, 1999.

L. Nilsson, Efficient table lookup without inverse square roots for calculation of pair wise atomic interactions in classical simulations, Journal of computational chemistry, vol.30, issue.9, p.25, 2009.

W. G. Noid, Perspective: Coarse-grained models for biomolecular systems, The Journal of chemical physics, vol.139, issue.9, p.20, 2013.

T. Vladimir-v-palyulin, R. Ala-nissila, and . Metzler, Polymer translocation: the first two decades and the recent diversification, Soft matter, vol.10, issue.45, pp.9016-9037, 2014.

D. Panja, T. Gerard, A. B. Barkema, and . Kolomeisky, Through the eye of the needle: recent advances in understanding biopolymer translocation, Journal of Physics: Condensed Matter, vol.25, issue.41, p.413101, 2013.

E. Paquet, . Herna, and . Viktor, Molecular dynamics, monte carlo simulations, and langevin dynamics: a computational review, BioMed research international, 2015.

J. Park and A. Heyden, Solving the equations of motion for mixed atomistic and coarse-grained systems, Molecular Simulation, vol.35, issue.10-11, pp.962-973, 2009.

I. Pasichnyk and B. Duenweg, Coulomb interactions via local dynamics: a molecular-dynamics algorithm, Journal of Physics: Condensed Matter, vol.16, issue.38

. S3999-s4020, , p.28, 2004.

M. Patra, M. Karttunen, . Marja-t-hyvönen, P. Falck, I. Lindqvist et al., Molecular dynamics simulations of lipid bilayers: major artifacts due to truncating electrostatic interactions, Biophysical journal, vol.84, issue.6, pp.3636-3645, 2003.

R. Juan, K. Perilla, and . Schulten, Physical properties of the hiv-1 capsid from all-atom molecular dynamics simulations, Nature communications, vol.8, p.15959, 2017.

. Henrik-g-petersen, Accuracy and efficiency of the particle mesh ewald method, The Journal of chemical physics, vol.103, issue.9, p.63, 1995.

R. James-c-phillips, W. Braun, J. Wang, E. Gumbart, E. Tajkhorshid et al., Scalable molecular dynamics with namd, Journal of computational chemistry, vol.26, issue.16, pp.1781-1802, 2005.

S. Piana, D. E. John-l-klepeis, and . Shaw, Assessing the accuracy of physical models used in protein-folding simulations: quantitative evidence from long molecular dynamics simulations, Current opinion in structural biology, vol.24, pp.98-105, 2014.

C. T. Levi, R. Pierce, C. Salomon-ferrer, F. Augusto, . De-oliveira et al., Routine access to millisecond time scale events with accelerated molecular dynamics, Journal of chemical theory and computation, vol.8, issue.9, pp.2997-3002, 2012.

S. Plimpton, Fast Parallel Algorithms for Short-Range Molecular Dynamics, Journal of Computational Physics, vol.117, issue.1, pp.1-19, 1995.

S. Plimpton, R. Pollock, and M. J. Stevens, Particle Mesh Ewald and rRESPA for Parallel Molecular Dynamics Simulations, Proceedings of the Eighth Siam Conference on Parallel Processing for Scientific Computing, p.112, 1997.

S. Plimpton, P. Crozier, and A. Thompson, Lammps-large-scale atomic/molecular massively parallel simulator, vol.18, 2007.

E. L. Pollock and J. Glosli, Comments on p3m, fmm, and the ewald method for large periodic coulombic systems, Computer Physics Communications, vol.95, issue.2-3, p.27, 1996.

M. Praprotnik, S. Matysiak, L. D. Site, K. Kremer, and C. Clementi, Adaptive resolution simulation of liquid water, Journal of Physics: Condensed Matter, vol.19, issue.29, p.292201, 2007.

. Charles-m-rader, Discrete fourier transforms when the number of data samples is prime, Proceedings of the IEEE, vol.56, p.46, 1968.

C. J. Anthony-k-rappé, . Casewit, . Colwell, W. M. Wa-goddard-iii, and . Skiff, Uff, a full periodic table force field for molecular mechanics and molecular dynamics simulations, Journal of the American chemical society, vol.114, issue.25, pp.10024-10035, 1992.

S. Redon, N. Galoppo, and M. Lin, Adaptive dynamics of articulated bodies, In ACM Transactions on Graphics, vol.24, p.29, 2005.
URL : https://hal.archives-ouvertes.fr/inria-00390315

R. Rossi, M. Isorce, S. Morin, J. Flocard, K. Arumugam et al., Adaptive torsion-angle quasi-statics: a general simulation method with applications to protein structure analysis and design, Bioinformatics, vol.23, issue.13, pp.408-417, 2007.
URL : https://hal.archives-ouvertes.fr/inria-00390312

B. Roux and T. Simonson, Implicit solvent models, Biophysical chemistry, vol.78, issue.1-2, pp.1-20, 1999.

P. Rowghanian and A. Grosberg, Force-driven polymer translocation through a nanopore: An old problem revisited, The Journal of Physical Chemistry B, vol.115, issue.48, pp.14127-14135, 2011.

K. John-w-ruge and . Stüben, Algebraic multigrid. Multigrid methods, vol.3, p.49, 1987.

Y. Saad, Iterative methods for sparse linear systems, SIAM, p.50, 2003.

C. Sagui and T. Darden, Multigrid methods for classical molecular dynamics simulations of biomolecules, Journal of Chemical Physics, vol.114, issue.15, p.96, 2001.

C. Sagui and T. Darden, Multigrid methods for classical molecular dynamics simulations of biomolecules, The Journal of Chemical Physics, vol.114, issue.15, p.27, 2001.

T. Saito and T. Sakaue, Cis-trans dynamical asymmetry in driven polymer translocation, Physical Review E, vol.88, issue.4, p.129, 2013.

J. Serna, Symplectic integrators for hamiltonian problems: an overview, Acta numerica, vol.1, pp.243-286, 1992.

J. Sarabadani, T. Ikonen, H. Mökkönen, T. Ala-nissila, S. Carson et al., Driven translocation of a semi-flexible polymer through a nanopore, Scientific Reports, vol.7, issue.1, p.129, 2017.

T. Schlick, Molecular Modeling and Simulation: An Interdisciplinary Guide, vol.21, p.96, 2010.

T. Schlick, Molecular modeling and simulation: an interdisciplinary guide: an interdisciplinary guide, vol.21, p.17, 2010.

E. Kevin, M. Schmidt, and . Lee, Implementing the fast multipole method in three dimensions, Journal of Statistical Physics, vol.63, issue.5-6, p.27, 1991.

R. Hans, J. Schwarz, and . Waldvogel, Numerical analysis: a comprehensive introduction, p.101, 1989.

Y. Shapira, Note on the multigrid w-cycle, Journal of Computational and Applied Mathematics, vol.85, issue.2, pp.351-353, 1997.

K. K. Singh and S. Redon, Adaptively Restrained Molecular Dynamics in LAMMPS. Modelling and Simulation in Materials Science and Engineering, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01525253

K. K. Singh and S. Redon, Single-pass incremental force updates for adaptively restrained molecular dynamics, Journal of Computational Chemistry, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01635863

K. K. Singh, F. Dmitriy, S. Marin, and . Redon, Parallel adaptively restrained molecular dynamics, High Performance Computing & Simulation (HPCS, pp.308-314, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01591466

K. Sint, B. Wang, and P. Král, Selective ion passage through functionalized graphene nanopores, Journal of the American Chemical Society, vol.130, issue.49, pp.16448-16449, 2008.

D. Robert, I. Skeel, D. Tezcan, and . Hardy, Multiple grid methods for classical molecular dynamics, Journal of Computational Chemistry, vol.23, issue.6, p.27, 2002.

D. Robert, . Skeel, J. David, J. Hardy, and . Phillips, Correcting mesh-based force calculations to conserve both energy and momentum in molecular dynamics simulations, Journal of computational physics, vol.225, issue.1, 2007.

E. Slonkina and A. B. Kolomeisky, Polymer translocation through a long nanopore, The Journal of chemical physics, vol.118, issue.15, p.126, 2003.

V. Springel, D. M. Simon, A. White, C. S. Jenkins, N. Frenk et al., Simulations of the formation, evolution and clustering of galaxies and quasars, nature, vol.435, issue.7042, p.629, 2005.

G. Stoltz and Z. Trstanova, Stable and accurate schemes for langevin dynamics with general kinetic energies, p.136, 2016.

J. Arnold, . Storm, . Chen, C. Hw-zandbergen, and . Dekker, Translocation of doublestrand dna through a silicon oxide nanopore, Physical review E, vol.71, issue.5, p.129, 2005.

W. B. Streett, G. Tildesley, and . Saville, Multiple time-step methods in molecular dynamics, Molecular Physics, vol.35, issue.3, p.26, 1978.

M. Stürmer, H. Köstler, and U. Rüde, A fast full multigrid solver for applications in image processing, vol.15, p.49, 2008.

E. Myung, N. R. Suk, and . Aluru, Water transport through ultrathin graphene, The Journal of Physical Chemistry Letters, vol.1, issue.10, p.110, 2010.

H. Sun, Compass: an ab initio force-field optimized for condensed-phase applications overview with details on alkane and benzene compounds, The Journal of Physical Chemistry B, vol.102, issue.38, p.13, 1998.

W. Sung and . Park, Polymer translocation through a pore in a membrane, Physical review letters, vol.77, issue.4, p.128, 1996.

G. Sutmann and B. Steffen, A particle-particle particle-multigrid method for long-range interactions in molecular simulations, Computer physics communications, vol.169, issue.1-3, p.27, 2005.

G. Sutmann, P. Gibbon, and T. Lippert, Fast Methods for LongRange Interactions in Complex Systems. Forschungszentrum Jülich, p.107, 2011.

, Agilent Technologies, p.127, 2018.

, Oxford Nanopore Technologies, p.127, 2018.

U. Trottenberg, A. Cornelius-w-oosterlee, . Schuller, and . Multigrid, , p.107, 2000.

Z. Trstanova, Mathematical and algorithmic analysis of modified Langevin dynamics, p.137, 2016.
URL : https://hal.archives-ouvertes.fr/tel-01682721

Z. Trstanova and S. Redon, Estimating the speed-up of adaptively restrained langevin dynamics, Journal of Computational Physics, vol.336, pp.412-428, 2017.

. Mbbjm-tuckerman, J. Bruce, G. Berne, and . Martyna, Reversible multiple time scale molecular dynamics, The Journal of chemical physics, vol.97, issue.3, 1990.

, Are Magnus Bruaset Aslak Tveito and Are Magnus Bruaset. Numerical solution of partial differential equations on parallel computers, p.55, 2006.

T. Patrick, P. Underhill, and . Doyle, On the coarse-graining of polymers into bead-spring chains, Journal of non-newtonian fluid mechanics, vol.122, issue.1-3, p.130, 2004.

S. Adri-ct-van-duin, F. Dasgupta, W. Lorant, and . Goddard, Reaxff: a reactive force field for hydrocarbons, The Journal of Physical Chemistry A, vol.105, issue.41, p.12, 2001.

. Wilfred-f-van-gunsteren, J. C. Herman, and . Berendsen, Computer simulation of molecular dynamics: Methodology, applications, and perspectives in chemistry

, Angewandte Chemie International Edition, vol.29, issue.9, p.26, 1990.

M. Bala, R. Venkatesan, and . Bashir, Nanopore sensors for nucleic acid analysis, Nature nanotechnology, vol.6, issue.10, p.126, 2011.

L. Verlet, Computer" experiments" on classical fluids. i. thermodynamical properties of lennard-jones molecules, Physical review, vol.159, issue.1, p.25, 1967.

J. Wang, R. M. Wolf, J. W. Caldwell, D. Peter-a-kollman, and . Case, Development and testing of a general amber force field, Journal of computational chemistry, vol.25, issue.9, p.11, 2004.

M. Wanunu, J. Sutin, B. Mcnally, A. Chow, and A. Meller, Dna translocation governed by interactions with solid-state nanopores, Biophysical journal, vol.95, issue.10, p.129, 2008.
DOI : 10.1529/biophysj.108.140475
URL : https://doi.org/10.1529/biophysj.108.140475

D. Wei, W. Yang, X. Jin, and Q. Liao, Unforced translocation of a polymer chain through a nanopore: The solvent effect, The Journal of chemical physics, vol.126, issue.20, p.128, 2007.

M. David-b-wells, J. Belkin, A. Comer, and . Aksimentiev, Assessing graphene nanopores for sequencing dna, Nano letters, vol.12, issue.8, p.126, 2012.

P. Wesseling, Cell-centered multigrid for interface problems, Journal of Computational Physics, vol.79, issue.1, p.54, 1988.
DOI : 10.1016/0021-9991(88)90005-8
URL : https://repository.tudelft.nl/islandora/object/uuid%3Afc882835-f4c6-4225-98ac-cc8e3da48dff/datastream/OBJ/download

P. Wesseling and ;. Va, Introduction to multigrid methods, 1995.

D. Wolf, . Keblinski, J. Sr-phillpot, and . Eggebrecht, Exact method for the simulation of coulombic systems by spherically truncated

, The Journal of chemical physics, vol.110, issue.17, p.28, 1999.

L. Yang, C. Tan, M. Hsieh, J. Wang, Y. Duan et al., New-generation amber united-atom force field, The journal of physical chemistry B, vol.110, issue.26, p.20, 2006.
DOI : 10.1021/jp060163v

Q. Ying-hua, L. Kun, C. Wei-yu, S. Wei, T. Qi-yan et al., Ion and water transport in charge-modified graphene nanopores, Chinese Physics B, vol.24, issue.10, p.110, 2015.

R. Yokota, . Lorena, and . Barba, A tuned and scalable fast multipole method as a preeminent algorithm for exascale systems, The International Journal of High Performance Computing Applications, vol.26, issue.4, p.27, 2012.
DOI : 10.1177/1094342011429952
URL : http://arxiv.org/pdf/1106.2176

B. Zagrovic, E. J. Sorin, and V. Pande, ?-hairpin folding simulations in atomistic detail using an implicit solvent model1, Journal of molecular biology, vol.313, issue.1, p.22, 2001.
DOI : 10.1006/jmbi.2001.5033