2021
DOI: 10.1021/acs.jpcb.1c01120
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Introducing Memory in Coarse-Grained Molecular Simulations

Abstract: Preserving the correct dynamics at the coarse-grained (CG) level is a pressing problem in the development of systematic CG models in soft matter simulation. Starting from the seminal idea of simple time-scale mapping, there have been many efforts over the years toward establishing a meticulous connection between the CG and fine-grained (FG) dynamics based on fundamental statistical mechanics approaches. One of the most successful attempts in this context has been the development of CG models based on the Mori−… Show more

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Cited by 79 publications
(89 citation statements)
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“…The field of coarse-grained description of the structures and dynamics of biomolecular systems is growing rapidly, both regarding the theoretical development and the scope of applications, and has advanced considerably since the seminal work by Levitt and Warshel [ 11 ]. A solid theoretical foundation of this approach has been provided by the Mori–Zwanzig theory of the projection operator [ 15 , 32 , 33 ], with which the effective equations of motion of the coarse-grained degrees of freedom could be derived [ 16 , 17 , 18 , 34 ] (Equation ( 1 )). With this derivation, it is clear that the PMF of the system should be considered as the potential energy in the equations of motion, which has pave the way towards the physics-based systematic development of CG force fields, similar to the Born–Oppenheimer approximation, which enables us to express the Potential Energy Surface (PES) of a system solely in terms of the coordinates of the nuclei [ 6 ]; this has been the basis of the development of all-atom force fields.…”
Section: Discussionmentioning
confidence: 99%
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“…The field of coarse-grained description of the structures and dynamics of biomolecular systems is growing rapidly, both regarding the theoretical development and the scope of applications, and has advanced considerably since the seminal work by Levitt and Warshel [ 11 ]. A solid theoretical foundation of this approach has been provided by the Mori–Zwanzig theory of the projection operator [ 15 , 32 , 33 ], with which the effective equations of motion of the coarse-grained degrees of freedom could be derived [ 16 , 17 , 18 , 34 ] (Equation ( 1 )). With this derivation, it is clear that the PMF of the system should be considered as the potential energy in the equations of motion, which has pave the way towards the physics-based systematic development of CG force fields, similar to the Born–Oppenheimer approximation, which enables us to express the Potential Energy Surface (PES) of a system solely in terms of the coordinates of the nuclei [ 6 ]; this has been the basis of the development of all-atom force fields.…”
Section: Discussionmentioning
confidence: 99%
“…From Equation ( 1 ), it follows that the net motion of the CG degrees of freedom is governed by the mean forces (the forces averaged over the atoms that constitute the interaction sites), while the fine-grained degrees of freedom contribute to the motion of the CG degrees of freedom through the friction forces (which depend on the time correlation of the fluctuations of the forces acting on the sites) and the fluctuating forces. The friction forces depend on the whole history of the correlation between the fluctuating forces and the velocities of the coarse-grained centers [ 17 , 34 ]. A number of studies were carried out with liquids or simple polymers to determine the friction term exactly based on all-atom simulations.…”
Section: Theory and Methodologymentioning
confidence: 99%
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