Computational Modeling of Membrane Bilayers by Scott E. Feller (Eds.)

By Scott E. Feller (Eds.)

Present issues in Membranes presents a scientific, finished, and rigorous method of particular subject matters proper to the research of mobile membranes. each one quantity is a visitor edited compendium of membrane biology. Articles coated within the quantity contain *Discusses present nation of electrostatics in biomolecular simulations and destiny directions*Includes details on time and size scales in lipid bilayer simulations*Covers the character of lipid rafts

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In the former, the requirement for zero surface tension can be (and perhaps should be) imposed. As an example, Berger et al. (1997), when developing an early version of a lipid FF used in many GROMOS based simulations, found that their original parameters yielded a positive surface tension, and then reduced the charges of head groups to yield zero surface tension. Sonne et al. (2007) have recently reparameterized the partial charges of the CHARMM C27r FF to obtain zero surface tension of DPPC near the experimental surface area.

From Table 2, approximately half of the surface tension of alkane/vapor interfaces is attributable to long-range LJ terms. Once treated correctly, the surface tensions of alkanes are in excellent agreement with experiment. Both TIP3P and TIP4P-Ew underestimate the surface tension of water by 23% and 15%, respectively. The errors in surface tension of hexadecane/water are −10% for TIP3P and +8% for TIP4P-Ew. Hence, interactions of water and alkane that take place on the boundary of the acyl chains of the bilayer and waters solvating the head groups are reasonably, but not quantitatively, described, in the CHARMM lipid FF.

2007). However, reliance on condensed phase data alone leaves the LJ parameters underdetermined (MacKerell, 2001). This problem has been overcome by determining the relative values of the LJ parameters via high-level QM data of interactions of the model compounds with rare gases (Yin and MacKerell, 1996) while the absolute values are based on the reproduction of ex- 10 Klauda et al. , 2002; Yin and MacKerell, 1998). This approach is tedious because it requires supramolecular interactions involving rare gases; however, once satisfactory LJ parameters are optimized for atoms in a class of functional groups they typically can be directly transferred to other molecules with those functional groups without further optimization.

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