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Multilevel Summation Method in NAMD

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Long-range electrostatic interactions control macromolecular processes within living cells as prominent charges appear everywhere, such as in DNA or RNA, in membrane lipid head groups, and in ion channels. Reliable and efficient description of electrostatic interactions is crucial in molecular dynamics simulations of such processes. Recently a new mathematical approach for calculating electrostatic interactions, known as multilevel summation method (MSM), has been developed and programmed into NAMD 2.10 as reported here. Compared to the earlier decades-long approach, the particle-mesh Ewald (PME) method, MSM provides more flexibility as it permits non-periodic simulations like ones with asymmetric charge distributions across a membrane or of a water droplet with a protein folding inside. Furthermore, MSM is ideally suited for modern parallel computers, running, for example, simulations of large virus particles. More information here.