S. A. Adcock and J. A. Mccammon, Molecular Dynamics:?? Survey of Methods for Simulating the Activity of Proteins, Chemical Reviews, vol.106, issue.5, p.1589, 2006.
DOI : 10.1021/cr040426m

W. F. Van-gunsteren and H. J. Berendsen, Computer Simulation of Molecular Dynamics: Methodology, Applications, and Perspectives in Chemistry, Angewandte Chemie International Edition in English, vol.29, issue.9, p.992, 1990.
DOI : 10.1002/anie.199009921

D. Hamelberg, J. Mongan, and J. A. Mccammon, Accelerated molecular dynamics: A promising and efficient simulation method for biomolecules, The Journal of Chemical Physics, vol.23, issue.24, pp.11919-1089, 2004.
DOI : 10.2307/2346830

A. Barducci, G. Bussi, and M. Parrinello, Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method, Physical Review Letters, vol.100, issue.2, pp.20603-00608, 2008.
DOI : 10.1021/jp067873l

URL : http://arxiv.org/pdf/0803.3861

S. Riniker and W. F. Gunsteren, Mixing coarse-grained and fine-grained water in molecular dynamics simulations of a single system, The Journal of Chemical Physics, vol.9, issue.4, pp.44120-44140, 2012.
DOI : 10.1002/jcc.1078

C. W. Hopkins, S. Le-grand, R. C. Walker, and A. E. Roitberg, Long-Time-Step Molecular Dynamics through Hydrogen Mass Repartitioning, Journal of Chemical Theory and Computation, vol.11, issue.4, p.1864, 2015.
DOI : 10.1021/ct5010406

D. E. Shaw, M. M. Deneroff, R. O. Dror, J. S. Kuskin, R. H. Larson et al., Anton, a special-purpose machine for molecular dynamics simulation, Communications of the ACM, vol.51, issue.7, p.91, 2008.
DOI : 10.1145/1364782.1364802

URL : http://www.cs.cmu.edu/afs/cs.cmu.edu/academic/class/15869-f11/www/readings/shaw07_anton.pdf

I. G. Tironi, R. Sperb, P. E. Smith, and W. F. Van-gunsteren, A generalized reaction field method for molecular dynamics simulations, The Journal of Chemical Physics, vol.102, issue.13, p.5451, 1995.
DOI : 10.1016/0021-9991(91)90043-K

T. Darden, D. York, and L. Pedersen, ) method for Ewald sums in large systems, The Journal of Chemical Physics, vol.9, issue.12, pp.10089-1089, 1993.
DOI : 10.1126/science.2548279

C. J. Fennell and J. D. Gezelter, Is the Ewald summation still necessary? Pairwise alternatives to the accepted standard for long-range electrostatics, The Journal of Chemical Physics, vol.73, issue.23, pp.234104-1089, 2006.
DOI : 10.1016/S0009-2614(02)01754-2

Y. Yonezawa, I. Fukuda, N. Kamiya, H. Shimoyama, and H. Nakamura, Free Energy Landscapes of Alanine Dipeptide in Explicit Water Reproduced by the Force-Switching Wolf Method, Journal of Chemical Theory and Computation, vol.7, issue.5, p.1484, 2011.
DOI : 10.1021/ct100357p

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, pp.2581-2598, 2012.
DOI : 10.1016/j.jcp.2011.12.006

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

F. Saiz and M. Gamero-castao, Amorphization of silicon induced by nanodroplet impact: A molecular dynamics study, Journal of Applied Physics, vol.112, issue.5, p.54302, 2012.
DOI : 10.1088/0953-8984/16/46/003

F. Saiz and M. Gamero-castao, Molecular dynamics of nanodroplet impact: The effect of the projectile???s molecular mass on sputtering, AIP Advances, vol.6, issue.6, p.65319, 2016.
DOI : 10.1134/S0036023610130036

A. Grossfield and D. M. Zuckerman, Annual reports in computational chemistry 5, 2009.

D. M. Zuckerman, Annual review of biophysics 40, p.41, 2011.

E. Lyman and D. M. Zuckerman, The journal of physical chemistry, p.12876, 2007.

T. D. Romo and A. Grossfield, Unknown Unknowns: the Challenge of Systematic and Statistical Error in Molecular Dynamics Simulations, Biophysical Journal, vol.106, issue.8, p.1553, 2014.
DOI : 10.1016/j.bpj.2014.03.007