Coupling Coarse-Grained to Fine-Grained Models via Hamiltonian Replica Exchange

Liu, Yang; Pezeshkian, Weria; Barnoud, Jonathan; Vries, Alex H. de; Marrink, Siewert J.

doi:10.1021/acs.jctc.0c00429

Cited by 10 publications

(9 citation statements)

References 51 publications

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“…The exchange is accepted based on the probability

expressed by Equation ( 15 ):

with

where

is the potential energy function (including the restraining potential) corresponding to the

trajectory, and

denotes the variables of the respective conformation of this trajectory at the attempted exchange point. A variant of HREMD was developed recently [ 215 ] for mixed-resolution MD simulations with the MARTINI [ 66 ] and GROMOS [ 216 ] force fields.…”

Section: Theory and Methodologymentioning

confidence: 99%

Theory and Practice of Coarse-Grained Molecular Dynamics of Biologically Important Systems

et al. 2021

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Molecular dynamics with coarse-grained models is nowadays extensively used to simulate biomolecular systems at large time and size scales, compared to those accessible to all-atom molecular dynamics. In this review article, we describe the physical basis of coarse-grained molecular dynamics, the coarse-grained force fields, the equations of motion and the respective numerical integration algorithms, and selected practical applications of coarse-grained molecular dynamics. We demonstrate that the motion of coarse-grained sites is governed by the potential of mean force and the friction and stochastic forces, resulting from integrating out the secondary degrees of freedom. Consequently, Langevin dynamics is a natural means of describing the motion of a system at the coarse-grained level and the potential of mean force is the physical basis of the coarse-grained force fields. Moreover, the choice of coarse-grained variables and the fact that coarse-grained sites often do not have spherical symmetry implies a non-diagonal inertia tensor. We describe selected coarse-grained models used in molecular dynamics simulations, including the most popular MARTINI model developed by Marrink’s group and the UNICORN model of biological macromolecules developed in our laboratory. We conclude by discussing examples of the application of coarse-grained molecular dynamics to study biologically important processes.

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“…The exchange is accepted based on the probability

expressed by Equation ( 15 ):

with

where

is the potential energy function (including the restraining potential) corresponding to the

trajectory, and

Section: Theory and Methodologymentioning

confidence: 99%

Theory and Practice of Coarse-Grained Molecular Dynamics of Biologically Important Systems

et al. 2021

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“…It was highly effective in simulate reversible transitions of small β-hairpins and helical IDPs [34,124,125] and proved instrumental in further refinement of a GBMV2 implicit solvent protein force field for both ordered and disordered peptides [126]. Very recently, MSES was also observed to be effective in sampling the cis-trans transitions of lutein by coupling the atomistic model with the Martini CG model [127]. Nonetheless, the application of MSES to larger and more complex proteins has proven more challenging than originally expected, apparently due to the difficulty in effective coupling of CG and atomistic conformational fluctuations of a larger protein.…”

Section: Collective Variables-free Sampling Methods and Optimizationmentioning

confidence: 99%

Advanced Sampling Methods for Multiscale Simulation of Disordered Proteins and Dynamic Interactions

Gong

Chen

2021

Biomolecules

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Intrinsically disordered proteins (IDPs) are highly prevalent and play important roles in biology and human diseases. It is now also recognized that many IDPs remain dynamic even in specific complexes and functional assemblies. Computer simulations are essential for deriving a molecular description of the disordered protein ensembles and dynamic interactions for a mechanistic understanding of IDPs in biology, diseases, and therapeutics. Here, we provide an in-depth review of recent advances in the multi-scale simulation of disordered protein states, with a particular emphasis on the development and application of advanced sampling techniques for studying IDPs. These techniques are critical for adequate sampling of the manifold functionally relevant conformational spaces of IDPs. Together with dramatically improved protein force fields, these advanced simulation approaches have achieved substantial success and demonstrated significant promise towards the quantitative and predictive modeling of IDPs and their dynamic interactions. We will also discuss important challenges remaining in the atomistic simulation of larger systems and how various coarse-grained approaches may help to bridge the remaining gaps in the accessible time- and length-scales of IDP simulations.

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“…The system is partitioned into two subsystems, that is, AA and CG. The crux of the method is that each subsystem interacts with itself at its corresponding level of description and that the interaction between the subsystems is at the CG level using the VS multiscale approach. − It was previously shown that the VS multiscale method can properly reproduce the potentials of mean force (PMFs) between pairs of apolar amino acid side-chain analogs, yet failed to reproduce correct PMFs for the polar and charged AA solutes in the CG solvent . Therefore, to avoid polar resolution interfaces, we propose a dual resolution membrane structure with the AA–CG interface at the interleaflet region, constituting an apolar environment, illustrated in Figure .…”

Section: Methodsmentioning

confidence: 99%

Capturing Membrane Phase Separation by Dual Resolution Molecular Dynamics Simulations

Liu

Vries

Pezeshkian

et al. 2021

J. Chem. Theory Comput.

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Understanding the lateral organization in plasma membranes remains an open problem and is of great interest to many researchers. Model membranes consisting of coexisting domains are commonly used as simplified models of plasma membranes. The coarse-grained (CG) Martini force field has successfully captured spontaneous separation of ternary membranes into a liquid-disordered and a liquid-ordered domain. With all-atom (AA) models, however, phase separation is much harder to achieve due to the slow underlying dynamics. To remedy this problem, here, we apply the virtual site (VS) hybrid method on a ternary membrane composed of saturated lipids, unsaturated lipids, and cholesterol to investigate the phase separation. The VS scheme couples the two membrane leaflets at CG and AA resolution. We found that the rapid phase separation reached by the CG leaflet can accelerate and guide this process in the AA leaflet.

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Coupling Coarse-Grained to Fine-Grained Models via Hamiltonian Replica Exchange

Cited by 10 publications

References 51 publications

Theory and Practice of Coarse-Grained Molecular Dynamics of Biologically Important Systems

Theory and Practice of Coarse-Grained Molecular Dynamics of Biologically Important Systems

Advanced Sampling Methods for Multiscale Simulation of Disordered Proteins and Dynamic Interactions

Capturing Membrane Phase Separation by Dual Resolution Molecular Dynamics Simulations

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