A Critical Comparison of Biomembrane Force Fields: Structure and Dynamics of Model DMPC, POPC, and POPE Bilayers

2016 ◽  
Vol 120 (16) ◽  
pp. 3888-3903 ◽  
Author(s):  
Kristyna Pluhackova ◽  
Sonja A. Kirsch ◽  
Jing Han ◽  
Liping Sun ◽  
Zhenyan Jiang ◽  
...  
Keyword(s):  
Force Fields ◽  
Critical Comparison ◽  
Structure And Dynamics

Critical Comparison of Biomembrane Force Fields: Protein–Lipid Interactions at the Membrane Interface

2017 ◽  
Vol 13 (5) ◽  
pp. 2310-2321 ◽  
Author(s):  
Angelica Sandoval-Perez ◽  
Kristyna Pluhackova ◽  
Rainer A. Böckmann
Keyword(s):  
Force Fields ◽  
Membrane Interface ◽  
Lipid Interactions ◽  
Critical Comparison

scholarly journals A Data-Driven Dimensionality Reduction Approach to Compare and Classify Lipid Force Fields

2021 ◽  
Author(s):  
Riccardo Capelli ◽  
Andrea Gardin ◽  
Charly Empereur-mot ◽  
Giovanni Doni ◽  
Giovanni M. Pavan
Keyword(s):  
Phase Transition ◽  
Force Fields ◽  
Coarse Grained ◽  
High Dimensional ◽  
Crucial Point ◽  
Structure And Dynamics ◽  
Intrinsic Resolution ◽  
Explicit Solvent ◽  
Gel Phase ◽  
Dynamics Simulations

<div><div><div><p>Molecular dynamics simulations of all-atom and coarse-grained lipid bilayer models are increasingly used to obtain insights useful for understanding the structural dynamics of these assemblies. In this context, one crucial point concerns the comparison of the performance and accuracy of classical force fields (FFs), which sometimes remains elusive. To date, the assessments performed on different classical potentials are mostly based on the comparison with experimental observables, which typically regard average properties. However, local differences of structure and dynamics, which are poorly captured by average measurements, can make a difference, but these are non-trivial to catch. Here we propose an agnostic way to compare different FFs at different resolutions (atomistic, united-atom, and coarse-grained), by means of a high-dimensional similarity metrics built on the framework of Smooth Overlap of Atomic Positions (SOAP). We compare and classify a set of 13 force fields, modeling 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) bilayers. Our SOAP kernels-based metrics allows us to compare, discriminate and correlate different force fields at different model resolutions in an unbiased, high-dimensional way. This also captures differences between FFs in modeling non-average events (originating from local transitions), such as for example the liquid-to-gel phase transition in dipalmitoylphosphatidylcholine (DPPC) bilayers, for which our metrics allows to identify nucleation centers for the phase transition, highlighting some intrinsic resolution limitations in implicit vs. explicit solvent force fields.</p></div></div></div>

A critical comparison of coarse-grained structure-based approaches and atomic models of protein folding

2017 ◽  
Vol 19 (21) ◽  
pp. 13629-13639 ◽  
Author(s):  
Jie Hu ◽  
Tao Chen ◽  
Moye Wang ◽  
Hue Sun Chan ◽  
Zhuqing Zhang
Keyword(s):  
Protein Folding ◽  
Force Fields ◽  
Coarse Grained ◽  
Unfolded Proteins ◽  
Critical Comparison ◽  
Atomic Models ◽  
Atomic Force

The predicted dimension of unfolded proteins is quite different using native-centric Gō-like models and transferrable (non-structure-based) models based on current atomic force fields.

Force Fields for Studying the Structure and Dynamics of Ionic Liquids: A Critical Review of Recent Developments

ChemPhysChem ◽  
2012 ◽  
Vol 13 (7) ◽  
pp. 1625-1637 ◽  
Author(s):  
Florian Dommert ◽  
Katharina Wendler ◽  
Robert Berger ◽  
Luigi Delle Site ◽  
Christian Holm
Keyword(s):  
Ionic Liquids ◽  
Critical Review ◽  
Force Fields ◽  
Structure And Dynamics ◽  
Recent Developments
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