Performance of the general amber force field in modeling aqueous POPC membrane bilayers

Jójárt, Balázs and Martinek, Tamás (2007) Performance of the general amber force field in modeling aqueous POPC membrane bilayers. JOURNAL OF COMPUTATIONAL CHEMISTRY, 28 (12). pp. 2051-2058. ISSN 0192-8651

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Abstract

The aim of this work was to answer the question of whether the general amber force field (GAFF) is food enough to simulate fully hydrated POPC membrane bilayers. The test system contained 128 POPC and 2985 TIP3P water molecules. The equilibration was carried out in a nonarbitrary manner to reach the stable liquid-crystalline phase. The simulations were performed by using particle mesh Ewald electrostatics implemented in molecular dynamics packages Amberg (NPT ensembles) and NAMD2 (NP gamma T ensembles). The computational results were assessed against the following experimental membrane properties: (i) area per lipid, (ii) area compressibility modulus, (iii) order parameter, (iv) gauche conformations per acyl chain, (v) lateral diffusion coefficients, (vi) electron density profile, and (vii) bound water at the lipid/water interface. The analyses revealed that the tested force field combination approximates the experimental values at an unexpectedly good level when the NP gamma T ensemble is applied with a surface tension of 60 mN m(-1) per bilayer. It is concluded that the GAFF/TIP3P combination can be utilized for aqueous membrane bilayer simulations, as it provides acceptable accuracy for biomolecular modeling. (c) 2007 Wiley Periodicals, Inc.

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