References
- Karplus M, McCammon JA. Molecular dynamics simulations of biomolecules. Nat Struct Biol. 2002;9:646–652. doi: 10.1038/nsb0902-646
- Ewen JP, Heyes DM, Dini D. Advances in nonequilibrium molecular dynamics simulations of lubricants and additives. Friction. 2018;6:349–386. doi: 10.1007/s40544-018-0207-9
- Jorgensen WL, Maxwell DS, TiradoRives J. Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. J Am Chem Soc. 1996;118:11225–11236. doi: 10.1021/ja9621760
- Sun H. COMPASS: an ab initio force-field optimized for condensed-phase applications – overview with details on alkane and benzene compounds. J Phys Chem B. 1998;102:7338–7364. doi: 10.1021/jp980939v
- Sun H, Jin Z, Yang CW, et al. COMPASS II: extended coverage for polymer and drug-like molecule databases. J Mol Model. 2016;22:47. doi: 10.1007/s00894-016-2909-0
- Wang JM, Wolf RM, Caldwell JW, et al. Development and testing of a general amber force field. J Comput Chem. 2004;25:1157–1174. doi: 10.1002/jcc.20035
- Marrink SJ, Risselada HJ, Yefimov S, et al. The MARTINI force field: coarse grained model for biomolecular simulations. J Phys Chem B. 2007;111:7812–7824. doi: 10.1021/jp071097f
- Reith D, Putz M, Muller-Plathe F. Deriving effective mesoscale potentials from atomistic simulations. J Comput Chem. 2003;24:1624–1636. doi: 10.1002/jcc.10307
- Moore TC, Iacovella CR, McCabe C. Derivation of coarse-grained potentials via multistate iterative Boltzmann inversion. J Chem Phys. 2014;140:224104. doi: 10.1063/1.4880555
- Lyubartsev AP, Laaksonen A. Calculation of effective interaction potentials from radial distribution functions: a reverse Monte Carlo approach. Phys Rev E. 1995;52:3730–3737. doi: 10.1103/PhysRevE.52.3730
- Lyubartsev AP, Karttunen M, Vattulainen I, et al. On coarse-graining by the inverse Monte Carlo method: dissipative particle dynamics simulations made to a precise tool in soft matter modeling. Soft Mater. 2002;1:121–137. doi: 10.1081/SMTS-120016746
- Izvekov S, Voth GA. Multiscale coarse graining of liquid-state systems. J Chem Phys. 2005;123:134105. doi: 10.1063/1.2038787
- Izvekov S, Voth GA. Modeling real dynamics in the coarse-grained representation of condensed phase systems. J Chem Phys. 2006;125:151101. doi: 10.1063/1.2360580
- Junghans C, Praprotnik M, Kremer K. Transport properties controlled by a thermostat: an extended dissipative particle dynamics thermostat. Soft Matter. 2008;4:156–161. doi: 10.1039/B713568H
- Fu CC, Kulkarni PM, Shell MS, et al. A test of systematic coarse-graining of molecular dynamics simulations: transport properties. J Chem Phys. 2013;139:094107. doi: 10.1063/1.4819472
- Plimpton S. Fast parallel algorithms for short-range molecular-dynamics. J Comput Phys. 1995;117:1–19. doi: 10.1006/jcph.1995.1039
- https://lammps.sandia.gov/.
- Gao L, Fang W. Semi-bottom-up coarse graining of water based on microscopic simulations. J Chem Phys. 2011;135:184101. doi: 10.1063/1.3658500
- Kauzlaric D, Meier JT, Espanol P, et al. Bottom-up coarse-graining of a simple graphene model: the blob picture. J Chem Phys. 2011;134:064106. doi: 10.1063/1.3554395
- Ranjith SK, Patnaik BSV, Vedantam S. No-slip boundary condition in finite-size dissipative particle dynamics. J Comput Phys. 2013;232:174–188. doi: 10.1016/j.jcp.2012.07.046
- Espanol P, Warren P. Statistical-mechanics of dissipative particle dynamics. Europhys Lett. 1995;30:191–196. doi: 10.1209/0295-5075/30/4/001
- Black JE, Silva C GM, Klein C, et al. Perfluoropolyethers: development of an All-atom force field for molecular simulations and validation with new experimental vapor pressures and liquid densities. J Phys Chem B. 2017;121:6588–6600. doi: 10.1021/acs.jpcb.7b00891
- Fukuda M, Zhang H, Ishiguro T, et al. Structure-based coarse-graining for inhomogeneous liquid polymer systems. J Chem Phys. 2013;139:054901. doi: 10.1063/1.4817192
- Kobayashi T, Zhang H, Fukuzawa K, et al. Coarse-grained molecular dynamic simulations of nanometer-thick polar lubricant films sheared between solid surfaces with random roughness. IEEE Trans Magn. 2015;51:1–4. doi: 10.1109/TMAG.2015.2435023
- Izvekov S, Rice BM. On the importance of shear dissipative forces in coarse-grained dynamics of molecular liquids. Phys Chem Chem Phys. 2015;17:10795–10804. doi: 10.1039/C4CP06116K
- Tuckerman M, Berne BJ, Martyna GJ. Reversible multiple time scale molecular dynamics. J Chem Phys. 1992;97:1990–2001. doi: 10.1063/1.463137