Paper Citing NAMD - Abstract
Zhuang, Xiaohong; Makover, Judah R.; Im, Wonpil; Klauda, Jeffery B.
A systematic molecular dynamics simulation study of temperature dependent bilayer structural properties
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1838:2520-2529, OCT 2014
Although lipid force fields (FFs) used in molecular dynamics (MD) simulations have proved to be accurate, there has not been a systematic study on their accuracy over a range of temperatures. Motivated by the X-ray and neutron scattering measurements of common phosphatidylcholine (PC) bilayers (Kucerka et al. BBA. 1808: 2761, 2011), the CHARMM36 (C36) FF accuracy is tested in this work with MD simulations of six common PC lipid bilayers over a wide range of temperatures. The calculated scattering form factors and deuterium order parameters from the C36 MD simulations agree well with the X-ray, neutron, and NMR experimental data. There is excellent agreement between MD simulations and experimental estimates for the surface area per lipid, bilayer thickness (D-B), hydrophobiothickness (D-C), and lipid volume (V-L). The only minor discrepancy between simulation and experiment is a measure of (D-B - D-HH) / 2 where D-HH is the distance between the maxima in the electron density profile along the bilayer normal. Additional MD simulations with pure water and heptane over a range of temperatures provide explanations of possible reasons causing the minor deviation. Overall, the C36 FF is accurate for use with liquid crystalline PC bilayers of varying chain types and over biologically relevant temperatures. (C) 2014 Elsevier B.V. All rights reserved.
