A comparison of the potential energy parameters of aliphatic alkanes: molecular dynamics simulations of triacylglycerols in the alpha phase.
A comparison of six GROMOS parameter sets for aliphatic alkanes is presented using simulations of a triglyceride, trioctanoin, in the gel or alpha phase. It is found that the parameter set 43A2 results in a system that is rigid and close packed, forcing a collective tilt of the molecules, known experimentally to be disallowed. The parameter set 45A3-45 results in an expanded system where the molecules undergo a conformational change from the chair to tuning-fork form. The lamellae are fragmented, with the fragments shifted in the direction parallel to the layer normal. The newest parameter set 45A3, when used with either of two sets of partial charges for the glycerol ester group, retains the characteristics of the gel phase. The last parameter set tested, 45A3-45x12, also performs well when combined with either set of partial charges, although the system expands in the plane of the bilayer.
Chandrasekhar
Indira
I
Laboratory of Physical Chemistry, Swiss Federal Institute of Technology Zürich, ETH-Zentrum, 8092 Zurich, Switzerland. indira@igc.phys.chem.ethz.ch
van Gunsteren
Wilfred F
WF
D000473:Alkanes / Q000737:chemistry*; D055592:Biophysical Phenomena; D001703:Biophysics; D002210:Caprylates / Q000737:chemistry; D003198:Computer Simulation; D007700:Kinetics; D008051:Lipid Bilayers; D008823:Micelles; D011487:Protein Conformation; D013997:Time Factors; D014280:Triglycerides / Q000737:chemistry*
D000473:Alkanes; D002210:Caprylates; D008051:Lipid Bilayers; D008823:Micelles; D014280:Triglycerides; C003637:tricaprylin