Bayesian parametrization of coarse-grain dissipative dynamics models

The Journal of Chemical Physics
Alain Dequidt, Jose G Solano Canchaya

Abstract

We introduce a new bottom-up method for the optimization of dissipative coarse-grain models. The method is based on Bayesian optimization of the likelihood to reproduce a coarse-grained reference trajectory obtained from analysis of a higher resolution molecular dynamics trajectory. This new method is related to force matching techniques, but using the total force on each grain averaged on a coarse time step instead of instantaneous forces. It has the advantage of not being limited to pairwise short-range interactions in the coarse-grain model and also yields an estimation of the friction parameter controlling the dynamics. The theory supporting the method is exposed in a practical perspective, with an analytical solution for the optimal set of parameters. The method was first validated by using it on a system with a known optimum. The new method was then tested on a simple system: n-pentane. The local molecular structure of the optimized model is in excellent agreement with the reference system. An extension of the method allows to get also an excellent agreement for the equilibrium density. As for the dynamic properties, they are also very satisfactory, but more sensitive to the choice of the coarse-grain representation. The ...Continue Reading

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Citations

Aug 9, 2016·The Journal of Chemical Physics·José G Solano CanchayaPatrice Malfreyt
Apr 30, 2016·Soft Matter·Pep EspañolIgnacio Zúñiga
Apr 24, 2017·The Journal of Chemical Physics·Pep Español, Patrick B Warren
Nov 23, 2017·The Journal of Chemical Physics·Gérôme FaurePep Español
Nov 7, 2019·Physical Chemistry Chemical Physics : PCCP·Josep Bonet AvalosJohn K Brennan
Jan 3, 2019·The Journal of Chemical Physics·Gregor Deichmann, Nico F A van der Vegt
Dec 10, 2020·The Journal of Chemical Physics·Florent GoujonPatrice Malfreyt
May 14, 2021·The Journal of Physical Chemistry. B·Viktor KlippensteinNico F A van der Vegt
Apr 7, 2018·Journal of Chemical Theory and Computation·Florent GoujonPatrice Malfreyt
Sep 25, 2019·Journal of Chemical Information and Modeling·James L McDonaghEdward O Pyzer-Knapp
Aug 29, 2019·ACS Omega·Kévin KempferPatrice Malfreyt

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