Uncertainty Quantification for Molecular Dynamics

Patrone, Paul N.; Dienstfrey, Andrew

doi:10.48550/arxiv.1801.02483

Cited by 2 publications

(2 citation statements)

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“…While much of the history of molecular simulation has focused on quantifying the impact of statistical uncertainty, [123][124][125] critical studies over the last decade [126][127][128][129][130][131][132][133][134][135] have improved our ability to quantify and propagate predictive uncertainty in molecular mechanics force elds by quantifying contributions from model uncertainty-which is frequently the major source of predictive uncertainty in applications of interest. While most attention has been focused on the continuous parameters of the force eld model with xed model form, some progress has been made in discrete model selection among candidate model forms.…”

Section: Espaloma Can Enable Bayesian Force Eld Parameterization And...mentioning

confidence: 99%

End-to-end differentiable construction of molecular mechanics force fields

et al. 2022

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Section: Espaloma Can Enable Bayesian Force Eld Parameterization And...mentioning

confidence: 99%

End-to-end differentiable construction of molecular mechanics force fields

et al. 2022

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“…The answer lies in the calibration of the temperature in all-atom MD simulation software and the approximate nature of the model systems which can be a subject of worthy debate but we degress for now. We focus on the reality of our investigations of an un-real model system [141,142] with the raw data presented here to avoid exaggeration and hype and for interested readers to reproduce, test, and develop it further. One should consider these temperatures as a guide rather than its quantitative measure for low to high range in order to assess the response of the protein structure.…”

Section: Molecular Dynamics (Md)mentioning

confidence: 99%

Molecular simulations of voltage-gated proton-selective channel

Boonamnaj

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Voltage-gated proton-selective channels (Hv1) are a membrane protein that permeates proton across cell membranes. They play an important role in various physiological processes. Hv1 was found as a dimer in membranes. Molecular mechanisms underlying the proton conduction of Hv1 have been a subject of intense research but is still remained unclear. In this study, molecular dynamics (MD) simulations of Hv1 were carried out to gain better understanding of the structure-function relationship. The first part of this thesis involved with an investigation of the role of the C-terminal domain (CTD) in stabilizing the dimer structure of Hv1. MD data showed the stability of the dimer structure depended on intersubunit interactions between amino acids located on the CTD. In the second part, an effect of ionization state of the charged residues on voltage-sensing domain (VSD) was examined. Upon changes in protonation states of conserved acid residues in the pore, conformational changes of the VSD were observed, affecting the size and hydration properties of the aqueous pore in Hv1. This study showed the orientation of water molecules in the pore. It was proposed that water molecules in the upper pore oriented its dipole vector in an opposite direction to those in the lower pore. The water orientation in the upper and lower pore was swapped as a result of changing the protonation state. In the last part, thermal-induced conformational changes of the CTD were investigated using coarse-grained Monte Carlo (CGMC) and all-atom MD simulations. As temperature increased, the CTD maintained its globular conformations in its native phase but it expanded in denatured phase. The results obtained from CGMC were compatible with the MD results demonstarting an efficiency of the CGMC approach.

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Uncertainty Quantification for Molecular Dynamics

Cited by 2 publications

References 91 publications

End-to-end differentiable construction of molecular mechanics force fields

End-to-end differentiable construction of molecular mechanics force fields

Molecular simulations of voltage-gated proton-selective channel

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