January 30, 2014 | Callum J. Dickson, Benjamin D. Madej, Age A. Skjevik, Robin M. Betz, Knut Teigen, Ian R. Gould, and Ross C. Walker
Lipid14 is an updated AMBER lipid force field that enables tensionless simulation of various lipid types. It is modular, allowing combinations of head and tail groups to create different lipid types. The Lennard-Jones and torsion parameters of both head and tail groups have been revised, and partial charges have been recalculated. The force field has been validated by simulating bilayers of six different lipid types for 0.5 μs each without applying surface tension, showing favorable agreement with experimental data for properties such as area per lipid, volume per lipid, bilayer thickness, NMR order parameters, scattering data, and lipid lateral diffusion. The force field is compatible with other AMBER force fields, including the General Amber Force Field and the ff99SB protein force field.
The Lipid14 force field was developed by refining hydrocarbon parameters to better reproduce thermodynamic and dynamic properties of alkane chains. This involved modifying Lennard-Jones and torsion parameters to match experimental values for heat of vaporization and density. The parameters were also adjusted to improve agreement with experimental data for the heat of vaporization and density of cis-2-hexene, cis-5-decene, and cis-7-pentadecene. The parameters were further refined to improve agreement with experimental data for the density of alkane chains.
The head group parameters were adjusted to better reproduce experimental data for the heat of vaporization of methyl acetate. The Lennard-Jones well-depths of the carbonyl oxygen, carbonyl carbon, and ester oxygen atoms were scaled to improve agreement with experimental data. The parameters were also applied to oxygen atoms in the phosphate region.
The Lipid14 force field was validated by simulating bilayers of six different lipid types for 0.5 μs each without applying surface tension. The results showed favorable agreement with experimental data for properties such as area per lipid, volume per lipid, bilayer thickness, NMR order parameters, scattering data, and lipid lateral diffusion. The results also showed that the bilayers were in the correct Lα-phase. The volume per lipid was calculated using the dimensions of the simulation box and the volume of a water molecule. The results showed that the volume per lipid was within 5% of experimental values.
The isothermal area compressibility modulus, K_A, was calculated from the fluctuation in the area per lipid. The results showed that K_A values fell close to experiment, with experimental values falling within the standard deviation of DMPC, DPPC, DOPC, and POPC simulation results. The POPE value came out high, indicating that this system was slightly too ordered.
The membrane thickness was examined by calculating D_HH, the peak-to-peak distance, from electron density profiles of the membranes. The results showed satisfactory agreement with experiment for all lipids, though the POPE value was a little high, indicating that this systemLipid14 is an updated AMBER lipid force field that enables tensionless simulation of various lipid types. It is modular, allowing combinations of head and tail groups to create different lipid types. The Lennard-Jones and torsion parameters of both head and tail groups have been revised, and partial charges have been recalculated. The force field has been validated by simulating bilayers of six different lipid types for 0.5 μs each without applying surface tension, showing favorable agreement with experimental data for properties such as area per lipid, volume per lipid, bilayer thickness, NMR order parameters, scattering data, and lipid lateral diffusion. The force field is compatible with other AMBER force fields, including the General Amber Force Field and the ff99SB protein force field.
The Lipid14 force field was developed by refining hydrocarbon parameters to better reproduce thermodynamic and dynamic properties of alkane chains. This involved modifying Lennard-Jones and torsion parameters to match experimental values for heat of vaporization and density. The parameters were also adjusted to improve agreement with experimental data for the heat of vaporization and density of cis-2-hexene, cis-5-decene, and cis-7-pentadecene. The parameters were further refined to improve agreement with experimental data for the density of alkane chains.
The head group parameters were adjusted to better reproduce experimental data for the heat of vaporization of methyl acetate. The Lennard-Jones well-depths of the carbonyl oxygen, carbonyl carbon, and ester oxygen atoms were scaled to improve agreement with experimental data. The parameters were also applied to oxygen atoms in the phosphate region.
The Lipid14 force field was validated by simulating bilayers of six different lipid types for 0.5 μs each without applying surface tension. The results showed favorable agreement with experimental data for properties such as area per lipid, volume per lipid, bilayer thickness, NMR order parameters, scattering data, and lipid lateral diffusion. The results also showed that the bilayers were in the correct Lα-phase. The volume per lipid was calculated using the dimensions of the simulation box and the volume of a water molecule. The results showed that the volume per lipid was within 5% of experimental values.
The isothermal area compressibility modulus, K_A, was calculated from the fluctuation in the area per lipid. The results showed that K_A values fell close to experiment, with experimental values falling within the standard deviation of DMPC, DPPC, DOPC, and POPC simulation results. The POPE value came out high, indicating that this system was slightly too ordered.
The membrane thickness was examined by calculating D_HH, the peak-to-peak distance, from electron density profiles of the membranes. The results showed satisfactory agreement with experiment for all lipids, though the POPE value was a little high, indicating that this system