R. Hockney and J. Eastwood, Computer Simulation Using Particles (Institute of Physics, 1992.

J. Monaghan, Smoothed particle hydrodynamics, Reports on Progress in Physics, vol.68, issue.8, p.1703, 2005.
DOI : 10.1088/0034-4885/68/8/R01

O. Etzmuss, J. Gross, and W. Strasser, Deriving a particle system from continuum mechanics for the animation of deformable objects, IEEE Transactions on Visualization and Computer Graphics, vol.9, issue.4, p.538, 2003.
DOI : 10.1109/TVCG.2003.1260747

J. Izaguirre, S. Reich, and R. Skeel, Longer time steps for molecular dynamics, The Journal of Chemical Physics, vol.110, issue.20, p.9853, 1999.
DOI : 10.1063/1.478995

K. Feenstra, B. Hess, and H. Berendsen, Improving efficiency of large time-scale molecular dynamics simulations of hydrogen-rich systems, Journal of Computational Chemistry, vol.22, issue.8, p.786, 1999.
DOI : 10.1002/(SICI)1096-987X(199906)20:8<786::AID-JCC5>3.0.CO;2-B

M. Preto and S. Tremaine, A Class of Symplectic Integrators with Adaptive Time Step for Separable Hamiltonian Systems, The Astronomical Journal, vol.118, issue.5, p.2532, 1999.
DOI : 10.1086/301102

F. Rao and M. Spichty, Thermodynamics and kinetics of large-time-step molecular dynamics, Journal of Computational Chemistry, vol.26, issue.5, p.475, 2012.
DOI : 10.1002/jcc.21990

P. Plechac and M. Rousset, Implicit Mass-matrix Penalization of Hamiltonian Dynamics with Application to Exact Sampling of Stiff Systems, Multiscale Modeling & Simulation, vol.8, issue.2, p.498, 2010.
DOI : 10.1137/08072348X

]. L. Greengard and V. Rokhlin, A fast algorithm for particle simulations, Journal of Computational Physics, vol.73, issue.2, p.325, 1987.
DOI : 10.1016/0021-9991(87)90140-9

P. B. Callahan, S. R. Kosaraju, and J. Assoc, A decomposition of multidimensional point sets with applications to k-nearest-neighbors and n-body potential fields, Journal of the ACM, vol.42, issue.1, p.67, 1995.
DOI : 10.1145/200836.200853

H. Lin and D. Truhlar, QM/MM: what have we learned, where are we, and where do we go from here?, Theoretical Chemistry Accounts, vol.109, issue.2, p.185, 2007.
DOI : 10.1007/s00214-006-0143-z

S. Marrink, H. Risselada, S. Yefimov, D. Tieleman, and A. Vries, The MARTINI Force Field:?? Coarse Grained Model for Biomolecular Simulations, The Journal of Physical Chemistry B, vol.111, issue.27, p.7812, 2007.
DOI : 10.1021/jp071097f

M. Praprotnik, L. Site, and K. Kremer, Multiscale Simulation of Soft Matter: From Scale Bridging to Adaptive Resolution, Annual Review of Physical Chemistry, vol.59, issue.1, p.545, 2008.
DOI : 10.1146/annurev.physchem.59.032607.093707

J. Park and A. Heyden, Solving the equations of motion for mixed atomistic and coarse-grained systems, Molecular Simulation, vol.105, issue.10-11, p.962, 2009.
DOI : 10.1021/ct700324x

B. Ensing, S. Nielsen, P. Moore, M. Klein, and M. Parrinello, Energy Conservation in Adaptive Hybrid Atomistic/Coarse-Grain Molecular Dynamics, Journal of Chemical Theory and Computation, vol.3, issue.3, p.1100, 2007.
DOI : 10.1021/ct600323n

B. R. Brooks, R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan et al., CHARMM: A program for macromolecular energy, minimization, and dynamics calculations, Journal of Computational Chemistry, vol.I, issue.2, p.187, 1983.
DOI : 10.1002/jcc.540040211

D. 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.
DOI : 10.1103/PhysRevB.42.9458

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, p.408, 2007.
DOI : 10.1093/bioinformatics/btm191

URL : https://hal.archives-ouvertes.fr/inria-00390312

M. Bosson, S. Grudinin, X. Bouju, and S. Redon, Interactive physically-based structural modeling of hydrocarbon systems, Journal of Computational Physics, vol.231, issue.6, p.2581, 2012.
DOI : 10.1016/j.jcp.2011.12.006

URL : https://hal.archives-ouvertes.fr/hal-00755542

E. Hairer, C. Lubich, and G. Wanner, Geometric Numerical Integration: Structure-Preserving Algorithms for Ordinary Differential Equations, Springer Series in Computational Mathematics, vol.31, 2006.

T. Lelievre, G. Stoltz, and M. Rousset, Free Energy Computations: A Mathematical Perspective, 2010.
DOI : 10.1142/p579

A. Rahman, Correlations in the Motion of Atoms in Liquid Argon, Physical Review, vol.136, issue.2A, p.405, 1964.
DOI : 10.1103/PhysRev.136.A405

Y. Sugita and Y. Okamoto, Replica-exchange molecular dynamics method for protein folding, Chemical Physics Letters, vol.314, issue.1-2, p.141, 1999.
DOI : 10.1016/S0009-2614(99)01123-9

A. Roitberg and R. Elber, Modeling side chains in peptides and proteins: Application of the locally enhanced sampling and the simulated annealing methods to find minimum energy conformations, The Journal of Chemical Physics, vol.95, issue.12, p.9277, 1991.
DOI : 10.1063/1.461157