Poster (P23)
Checking Compatibility of Different Model of Water with a United Atom Model of Lipid Membrane
Shakkira E.1, Snehasis Daschakraborty*2
Department of chemistry, Indian Institute of Technology Patna, Bihar.
1 1821ch09[at]iitp.ac.in
Cell membrane of Eukaryotes and Prokaryotes are composed of lipid bilayer- of which Phosphatidylcholine and Sphingomyelin are the major components. Structural variations in them introduce characteristic changes in their fluidity and diffusive properties. Presence of lipids with more unsaturated/short chain /branched fatty acids in the membrane somehow provide support for cold adaptation, which is the key for survival of psychrophiles at extreme cold condition. Lipid simulations are widely conducted with all atom, united atom and coarse-grained models. GROMOS forcefield is widely used in this regard as it reproduces many of the structural and dynamical properties of different lipid membrane. However, Gromos forcefield is developed to use with SPC water model. But in order to get insight into the lipid bilayer and the underlying structure and dynamics at low temperature (generally below 0o C) we need to use water models, like TIP4P/2005, which reproduces properties of water at low temperatures. This motivates us to check the compatibility of the more advanced water model with the existing GROMOS force field of lipid. Here, we have considered of DPPC and POPC lipid bilayer with five different models of water, SPC, TIP4P/2005, TIP4P-FB, TIP3P, and TIP3P-FB. The sensitivity of structure and dynamics of lipids has been assessed in our studies and the various simulated results are compared with the available experiments. This study, thereby, assist in judging the most suitable water model, except SPC model, for simulating lipid membrane at low temperature.
D. Poger, A. E. Mark, On the Validation of Molecular Dynamics Simulations of Saturated and Cis-Monounsaturated Phosphatidylcholine Lipid Bilayers: A Comparison with Experiment. J. Chem. Theory Comput. 6 (2010), 325.