Comment on “Isolating the non-polar contributions to the intermolecular potential for water-alkane interactions” [J. Chem. Phys. 141, 064905 (2014)]

McDaniel, Jesse G.; Yethiraj, Arun

doi:10.1063/1.4944978

Cited by 17 publications

(16 citation statements)

References 4 publications

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“…In comparison, Shirts & Pande (2005) showed that the chemical potentials of SPC, SPC/E, TIP3P, TIP4P, and TIP4P-Ew ranged from −6.10 to −7.05 kcal/mol, which are closer to the experimental estimates of −5.7 and −6.3 kcal/mol. Limitations of the force field combination rule and neglect of induced polarization have also been proposed to cause the solubility of water in alkane solvents to be underestimated ( Ballal et al, 2014 ; McDaniel & Yethiraj, 2016 ). Reparameterization of the alkane–water non-bonded parameters may be needed to capture the correct water permeability of the bilayer using these models.…”

Section: Discussionmentioning

confidence: 99%

Simulations of lipid bilayers using the CHARMM36 force field with the TIP3P-FB and TIP4P-FB water models

Sajadi¹,

Rowley²

2018

PeerJ

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The CHARMM36 force field for lipids is widely used in simulations of lipid bilayers. The CHARMM family of force fields were developed for use with the mTIP3P water model. This water model has an anomalously high dielectric constant and low viscosity, which limits its accuracy in the calculation of quantities like permeability coefficients. The TIP3P-FB and TIP4P-FB water models are more accurate in terms of the dielectric constant and transport properties, which could allow more accurate simulations of systems containing water and lipids. To test whether the CHARMM36 lipid force field is compatible with the TIP3P-FB and TIP4P-FB water models, we have performed simulations of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine bilayers. The calculated headgroup area, compressibility, order parameters, and X-ray form factors are in good agreement with the experimental values, indicating that these improved water models can be used with the CHARMM36 lipid force field without modification when calculating membrane physical properties. The water permeability predicted by these models is significantly different; the mTIP3P-model diffusion in solution and at the lipid–water interface is anomalously fast due to the spuriously low viscosity of mTIP3P-model water, but the potential of mean force of permeation is higher for the TIP3P-FB and TIP4P-FB models due to their high excess chemical potentials. As a result, the rates of water permeation calculated the FB water models are slower than the experimental value by a factor of 15–17, while simulations with the mTIP3P model only underestimate the water permeability by a factor of 3.

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Section: Discussionmentioning

confidence: 99%

Simulations of lipid bilayers using the CHARMM36 force field with the TIP3P-FB and TIP4P-FB water models

Sajadi¹,

Rowley²

2018

PeerJ

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show abstract

“…Limitations of the force field combination rule and neglect of induced polarization have also been proposed to cause the solubility of water in alkane solvents to be underestimated. 51,52 Reparameterization of the alkane-water non-bonded parameters may be needed to capture the correct water permeability of the bilayer.…”

Section: Water Permeabilitymentioning

confidence: 99%

The CHARMM36 Force Field for Lipids Can Be Used With More Accurate Water Models

Sajadi¹,

Rowley²

2018

Preprint

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The CHARMM36 force field for lipids is widely used in simulations of lipid bilayers. The CHARMM family of force fields were developed for use with the TIP3P water model. This water model has an anomalously high dielectric constant and low viscosity, which limits its accuracy in the calculation of quantities like permeability coefficients. The TIP3P-FB and TIP4P-FB water models are more accurate in terms of the dielectric constant and transport properties, which could allow more accurate simulations of systems containing water and lipids. To test whether the CHARMM36 lipid force field is compatible with the TIP3P-FB and TIP4P-FB water models, we have performed simulations of DPPC and POPC bilayers. The calculated headgroup area, compressibility, order parameters, and X-ray form factors are in good agreement with the experimental values, indicating that these improved water models can be used with the CHARMM36 lipid force field without modification. The water permeability predicted by these models is significantly different; the TIP3P-model diffusion in solution and at the lipid--water interface is anomalously fast due to the spuriously low viscosity of TIP3P-model water, but the PMF of permeation is higher for the TIP3P-FB and TIP4P-FB models due to their high excess chemical potentials.

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“…42 13 Limitations of the force field combination rule and neglect of induced polarization have also been proposed to cause the solubility of water in alkane solvents to be underestimated. 51,52 Reparameterization of the alkane-water non-bonded parameters may be needed to capture the correct water permeability of the bilayer.…”

Section: Water Permeabilitymentioning

confidence: 99%

“…TIP3P TIP3P-FB TIP4P-FB ρ / g cm −3 0.997 0.98 0.995 0.996 ∆H vap / kcal mol −1 10. 52 The CHARMM36 model for lipids was developed for use with the TIP3P water model.…”

Section: Introductionmentioning

confidence: 99%

The CHARMM36 Force Field for Lipids Can Be Used With More Accurate Water Models

Sajadi¹,

Rowley²

2018

Preprint

View full text Add to dashboard Cite

The CHARMM36 force field for lipids is widely used in simulations of lipid bilayers. The CHARMM family of force fields were developed for use with the TIP3P water model. This water model has an anomalously high dielectric constant and low viscosity, which limits its accuracy in the calculation of quantities like permeability coefficients. The TIP3P-FB and TIP4P-FB water models are more accurate in terms of the dielectric constant and transport properties, which could allow more accurate simulations of systems containing water and lipids. To test whether the CHARMM36 lipid force field is compatible with the TIP3P-FB and TIP4P-FB water models, we have performed simulations of DPPC and POPC bilayers. The calculated headgroup area, compressibility, order parameters, and X-ray form factors are in good agreement with the experimental values, indicating that these improved water models can be used with the CHARMM36 lipid force field without modification. The water permeability predicted by these models is significantly different; the TIP3P-model diffusion in solution and at the lipid-water interface is anomalously fast due to the spuriously low viscosity of TIP3P-model water, but the PMF of permeation is higher for the TIP3P-FB and a TIP4P-FB models due to their high excess chemical potentials.

show abstract

Comment on “Isolating the non-polar contributions to the intermolecular potential for water-alkane interactions” [J. Chem. Phys. 141, 064905 (2014)]

Cited by 17 publications

References 4 publications

Simulations of lipid bilayers using the CHARMM36 force field with the TIP3P-FB and TIP4P-FB water models

Simulations of lipid bilayers using the CHARMM36 force field with the TIP3P-FB and TIP4P-FB water models

The CHARMM36 Force Field for Lipids Can Be Used With More Accurate Water Models

The CHARMM36 Force Field for Lipids Can Be Used With More Accurate Water Models

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