Literature DB >> 33620214

Semi-automated Optimization of the CHARMM36 Lipid Force Field to Include Explicit Treatment of Long-Range Dispersion.

Yalun Yu1,2, Andreas Krämer2, Richard M Venable2, Andrew C Simmonett2, Alexander D MacKerell3, Jeffery B Klauda1,4, Richard W Pastor2, Bernard R Brooks2.   

Abstract

The development of the CHARMM lipid force field (FF) can be traced back to the early 1990s with its current version denoted CHARMM36 (C36). The parametrization of C36 utilized high-level quantum mechanical data and free energy calculations of model compounds before parameters were manually adjusted to yield agreement with experimental properties of lipid bilayers. While such manual fine-tuning of FF parameters is based on intuition and trial-and-error, automated methods can identify beneficial modifications of the parameters via their sensitivities and thereby guide the optimization process. This work introduces a semi-automated approach to reparametrize the CHARMM lipid FF with consistent inclusion of long-range dispersion through the Lennard-Jones particle-mesh Ewald (LJ-PME) approach. The optimization method is based on thermodynamic reweighting with regularization with respect to the C36 set. Two independent optimizations with different topology restrictions are presented. Targets of the optimizations are primarily liquid crystalline phase properties of lipid bilayers and the compression isotherm of monolayers. Pair correlation functions between water and lipid functional groups in aqueous solution are also included to address headgroup hydration. While the physics of the reweighting strategy itself is well-understood, applying it to heterogeneous, complex anisotropic systems poses additional challenges. These were overcome through careful selection of target properties and reweighting settings allowing for the successful incorporation of the explicit treatment of long-range dispersion, and we denote the newly optimized lipid force field as C36/LJ-PME. The current implementation of the optimization protocol will facilitate the future development of the CHARMM and related lipid force fields.

Entities:  

Year:  2021        PMID: 33620214      PMCID: PMC8059446          DOI: 10.1021/acs.jctc.0c01326

Source DB:  PubMed          Journal:  J Chem Theory Comput        ISSN: 1549-9618            Impact factor:   6.006


  77 in total

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Journal:  J Phys Chem B       Date:  2017-03-02       Impact factor: 2.991

5.  Update of the CHARMM36 United Atom Chain Model for Hydrocarbons and Phospholipids.

Authors:  Yalun Yu; Jeffery B Klauda
Journal:  J Phys Chem B       Date:  2020-07-22       Impact factor: 2.991

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Journal:  J Chem Theory Comput       Date:  2016-11-21       Impact factor: 6.006

8.  An extensive simulation study of lipid bilayer properties with different head groups, acyl chain lengths, and chain saturations.

Authors:  Xiaohong Zhuang; Eder M Dávila-Contreras; Andrew H Beaven; Wonpil Im; Jeffery B Klauda
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9.  Simulations of anionic lipid membranes: development of interaction-specific ion parameters and validation using NMR data.

Authors:  Richard M Venable; Yun Luo; Klaus Gawrisch; Benoît Roux; Richard W Pastor
Journal:  J Phys Chem B       Date:  2013-08-22       Impact factor: 2.991

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Journal:  Nature       Date:  2011-10-23       Impact factor: 49.962

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2.  Physical Characterization of Triolein and Implications for Its Role in Lipid Droplet Biogenesis.

Authors:  Siyoung Kim; Gregory A Voth
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3.  CHARMM36 Lipid Force Field with Explicit Treatment of Long-Range Dispersion: Parametrization and Validation for Phosphatidylethanolamine, Phosphatidylglycerol, and Ether Lipids.

Authors:  Yalun Yu; Andreas Krämer; Richard M Venable; Bernard R Brooks; Jeffery B Klauda; Richard W Pastor
Journal:  J Chem Theory Comput       Date:  2021-02-23       Impact factor: 6.006

4.  Recharging your fats: CHARMM36 parameters for neutral lipids triacylglycerol and diacylglycerol.

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6.  Accurate Simulations of Lipid Monolayers Require a Water Model with Correct Surface Tension.

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Journal:  J Chem Theory Comput       Date:  2022-02-08       Impact factor: 6.006

7.  Seipin transmembrane segments critically function in triglyceride nucleation and lipid droplet budding from the membrane.

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8.  Mechanical properties of anionic asymmetric bilayers from atomistic simulations.

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Journal:  J Chem Phys       Date:  2021-06-14       Impact factor: 4.304

  8 in total

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