513
Views
4
CrossRef citations to date
0
Altmetric
Articles

A generalized Newton iteration for computing the solution of the inverse Henderson problem

, &
Pages 1166-1190 | Received 26 Mar 2019, Accepted 28 Nov 2019, Published online: 16 Jan 2020

References

  • Potestio R, Peter C, Kremer K. Computer simulations of soft matter: linking the scales. Entropy. 2014;16:4199–4245. doi: 10.3390/e16084199
  • Henderson RL. A uniqueness theorem for fluid pair correlation functions. Phys Lett A. 1974;49:197–198. doi: 10.1016/0375-9601(74)90847-0
  • Ben-Naim A. Molecular theory of solutions. New York: Oxford University Press; 2006.
  • Hansen J-P, McDonald IR. Theory of simple liquids. 4th ed. Oxford: Academic Press; 2013.
  • Mirzoev A, Lyubartsev AP. MagiC: software package for multiscale modeling. J Chem Theory Comput. 2013;9:1512–1520. doi: 10.1021/ct301019v
  • Rühle V, Junghans C, Lukyanov A, et al. Versatile object-oriented toolkit for coarse-graining applications. J Chem Theory Comput. 2009;5:3211–3223. doi: 10.1021/ct900369w
  • Tóth G. Interactions from diffraction data: historical and comprehensive overview of simulation assisted methods. J Phys Condens Matter. 2007;19:335220.
  • Jörgens K. Linear integral operators. Boston: Pitman; 1982.
  • Ruelle D. Statistical mechanics: rigorous results. New York: W.A. Benjamin Publ.; 1969.
  • Hanke M. Fréchet differentiability of molecular distribution functions I. L∞ analysis. Lett Math Phys. 2018;108:285–306. doi: 10.1007/s11005-017-1009-0
  • Hanke M. Well-posedness of the iterative Boltzmann inversion. J Stat Phys. 2018;170:536–553. doi: 10.1007/s10955-017-1944-2
  • Schommers W. A pair potential for liquid rubidium from the pair correlation function. Phys Lett. 1973;43A:157–158. doi: 10.1016/0375-9601(73)90591-4
  • Soper AK. Empirical potential Monte Carlo simulation of fluid structure. Chem Phys. 1996;202:295–306. doi: 10.1016/0301-0104(95)00357-6
  • 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
  • Murtola T, Falck E, Karttunen M, et al. Coarse-grained model for phospholipid/cholesterol bilayer employing inverse Monte Carlo with thermodynamic constraints. J Chem Phys. 2007;126:075101.
  • Ivanizki D. Numerical analysis of the relation between interactions and structure in a molecular fluid. PhD Thesis. Johannes Gutenberg-Universität Mainz; 2015.
  • Levesque D, Weis JJ, Reatto L. Pair interaction from structural data for dense classical liquids. Phys Rev Lett. 1985;54:451–454. doi: 10.1103/PhysRevLett.54.451
  • Heinen M. Calculating particle pair potentials from fluid-state pair correlations: iterative Ornstein–Zernike inversion. J Comput Chem. 2018;39:1531–1543. doi: 10.1002/jcc.25225
  • Henrici P. Applied and computational complex analysis. Vol. 3. New York: John Wiley & Sons; 1986.
  • Abraham MJ, van der Spoel D, Lindahl E, et al. the Gromacs development team. Gromacs User Manual version 2016.3, www.gromacs.org (2017).
  • Hess B, Kutzner C, van der Spoel D, et al. GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation. J Chem Theory Comput. 2008;4:435–447. doi: 10.1021/ct700301q
  • Lyubartsev A, Mirzoev A, Chen L, et al Systematic coarse-graining of molecular models by the Newton inversion method. Faraday Discuss. 2010;144:43–56. doi: 10.1039/B901511F
  • Fu CC, Kulkarni PM, Shell MS, et al. A test of systematic coarse-graining of molecular dynamics simulations: thermodynamic properties. J Chem Phys. 2012;137:164106.
  • Jain S, Garde S, Kumar SK. Do inverse Monte Carlo algorithms yield thermodynamically consistent interaction potentials? Ind Eng Chem Res. 2006;45:5614–5618. doi: 10.1021/ie060042h
  • Reith D, Pütz M, Müller-Plathe F. Deriving effective mesoscale potentials from atomistic simulations. J Comput Chem. 2003;24:1624–1636. doi: 10.1002/jcc.10307
  • Wang H, Junghans C, Kremer K. Comparative atomistic and coarse-grained study of water: what do we lose by coarse-graining? Eur Phys J E. 2009;28:221–229. doi: 10.1140/epje/i2008-10413-5
  • Björck Å. Numerical methods for least squares problems. Philadelphia: SIAM; 1996.
  • Smit B. Phase diagrams of Lennard–Jones fluids. J Chem Phys. 1992;96:8639–8640. doi: 10.1063/1.462271
  • Hansen J-P, Verlet L. Phase transitions of the Lennard–Jones system. Phys Rev. 1969;184:151–161. doi: 10.1103/PhysRev.184.151
  • Schmidt PW, Tompson CW. X-ray scattering studies of simple fluids. In: Frisch HL and Salsburg ZW, editors. Simple Dense Fluids, New York: Academic Press; 1968. p. 31–110.
  • Tuckerman ME. Statistical mechanics: theory and molecular simulation. Oxford: Oxford University Press; 2010.
  • Mikolaj PG, Pings CJ. Structure of liquids. III. An X-ray diffraction study of fluid argon. J Chem Phys. 1967;46:1401–1411. doi: 10.1063/1.1840864

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.