scholarly journals Evaluating Coarse-Grained MARTINI Force-Fields for Capturing the Ripple Phase of Lipid Membranes

2021 ◽  
Author(s):  
Pradyumn Sharma ◽  
Rajat Desikan ◽  
K. Ganapathy Ayappa
Keyword(s):  
Lipid Membranes ◽  
Force Fields ◽  
Coarse Grained ◽  
Ripple Phase

scholarly journals Evaluating coarse-grained MARTINI force-fields for capturing the ripple phase of lipid membranes

2020 ◽  
Author(s):  
Pradyumn Sharma ◽  
Rajat Desikan ◽  
K. Ganapathy Ayappa
Keyword(s):  
Lipid Bilayers ◽  
Lipid Membranes ◽  
Liquid Crystalline ◽  
Intermediate Phase ◽  
Finite Size ◽  
Fluid Phase ◽  
Md Simulations ◽  
Coarse Grained ◽  
Lamellar Phases ◽  
Ripple Phase

AbstractPhospholipids, which are an integral component of cell membranes, exhibit a rich variety of lamellar phases modulated by temperature and composition. Molecular dynamics (MD) simulations have greatly enhanced our understanding of phospholipid membranes by capturing experimentally observed phases and phase transitions at molecular resolution. However, the ripple (Pβ′) membrane phase, observed as an intermediate phase below the main gel-to-liquid crystalline transition with some lipids, has been challenging to capture with MD simulations, both at all-atom and coarse-grained resolution. Here, we systematically assess the ability of five coarse-grained MARTINI 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) lipid force-field (FF) variants, parametrized to reproduce the DPPC gel and fluid phases, for their ability to capture the Pβ′ phase. Upon cooling from the fluid phase to below the phase transition temperature with smaller (380-lipid) and larger (> 2200-lipid) MARTINI and all-atom (CHARMM36 FF) DPPC lipid bilayers, we observed that smaller bilayers with both all-atom and MARTINI FFs sampled interdigitated Pβ′ and ripple-like states, respectively. However, while all-atom simulations of the larger DPPC membranes exhibited the formation of the Pβ′ phase, similar to previous studies, MARTINI membranes did not sample interdigitated ripple-like states at larger system sizes. We then demonstrated that the ripple-like states in smaller MARTINI membranes were kinetically-trapped structures caused by finite size effects rather than being representative of true Pβ′ phases. We showed that even a MARTINI FF variant that could capture the tilted Lβ′ gel phase, a prerequisite for stabilizing the Pβ′ phase, could not capture the rippled phase upon cooling. Our study reveals that the current MARTINI FFs may require specific re-parametrization of the interaction potentials to stabilize lipid interdigitation, a characteristic of the ripple phase.

Transferability of coarse-grained force fields: The polymer case

2008 ◽  
Vol 128 (6) ◽  
pp. 064904 ◽  
Author(s):  
Paola Carbone ◽  
Hossein Ali Karimi Varzaneh ◽  
Xiaoyu Chen ◽  
Florian Müller-Plathe
Keyword(s):  
Force Fields ◽  
Coarse Grained

scholarly journals A new protein nucleic-acid coarse-grained force field based on the UNRES and NARES-2P force fields

2018 ◽  
Vol 39 (28) ◽  
pp. 2360-2370 ◽  
Author(s):  
Adam K. Sieradzan ◽  
Artur Giełdoń ◽  
Yanping Yin ◽  
Yi He ◽  
Harold A. Scheraga ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Force Field ◽  
Force Fields ◽  
Coarse Grained ◽  
Protein Nucleic Acid ◽  
New Protein

Prediction of self-assemblies of sodium dodecyl sulfate and fragrance additives using coarse-grained force fields

2017 ◽  
Vol 23 (7) ◽  
Author(s):  
Chunwei Yang ◽  
Zhe Shen ◽  
Liang Wu ◽  
Haiqiu Tang ◽  
Lifeng Zhao ◽  
...  
Keyword(s):  
Sodium Dodecyl Sulfate ◽  
Force Fields ◽  
Sodium Dodecyl ◽  
Coarse Grained ◽  
Dodecyl Sulfate

Utilizing Machine Learning for Efficient Parameterization of Coarse Grained Molecular Force Fields

2019 ◽  
Vol 59 (10) ◽  
pp. 4278-4288 ◽  
Author(s):  
James L. McDonagh ◽  
Ardita Shkurti ◽  
David J. Bray ◽  
Richard L. Anderson ◽  
Edward O. Pyzer-Knapp
Keyword(s):  
Machine Learning ◽  
Force Fields ◽  
Coarse Grained ◽  
Molecular Force
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