Lipid simulations

Fig. 7.20 Variation in alignment of chains in lipid simulation with tilt angle [van der Ploeg and Berendsen 1932].

To date, a number of simulation studies have been performed on nucleic acids and proteins using both AMBER and CHARMM. A direct comparison of crystal simulations of bovine pancreatic trypsin inliibitor show that the two force fields behave similarly, although differences in solvent-protein interactions are evident [24]. Side-by-side tests have also been performed on a DNA duplex, showing both force fields to be in reasonable agreement with experiment although significant, and different, problems were evident in both cases [25]. It should be noted that as of the writing of this chapter revised versions of both the AMBER and CHARMM nucleic acid force fields had become available. Several simulations of membranes have been performed with the CHARMM force field for both saturated [26] and unsaturated [27] lipids. The availability of both protein and nucleic acid parameters in AMBER and CHARMM allows for protein-nucleic acid complexes to be studied with both force fields (see Chapter 20), whereas protein-lipid (see Chapter 21) and DNA-lipid simulations can also be performed with CHARMM. 

Marrink SJ, de Vries AH, Mark AE. Coarse grained model for semiquantitative lipid simulations. J. Phys. Chem. B 2004 108 750-760. 

Lipotoxicity due to accumulation of lipid simulation results 300 2 200-400 U/L >5 weeks... 

Program for Simulation of Biological and Organic Molecules) has been u.sed in a number of lipid simulations " ... 

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