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Impact of Dispersion Coefficient on Simulations of Proteins and Organic Liquids B

Bashardanesh, Zahedeh, van der Spoel, David
The Journal of physical chemistry 2018 v.122 no.33 pp. 8018-8027
coagulation, dispersibility, liquids, physical chemistry, proteins
In the context of studies of proteins under crowding conditions, it was found that there is a tendency of simulated proteins to coagulate in a seemingly unphysical manner. This points to an imbalance in the protein–protein or protein–water interactions. One way to resolve this is to strengthen the protein–water Lennard-Jones interactions. However, it has also been suggested that dispersion interactions may have been systematically overestimated in force fields due to parameterization with a short cutoff. Here, we test this proposition by performing simulations of liquids and of proteins in solution with systematically reduced C₆ (dispersion constant in a 12-6 Lennard-Jones potential) and evaluate the properties. We find that simulations of liquids with either a dispersion correction or explicit long-range Lennard-Jones interactions need little or no correction to the dispersion constant to reproduce the experimental density. For simulations of proteins, a significant reduction in the dispersion constant is needed to reduce the coagulation, however. Because the protein- and liquid force fields share atom types, at least to some extent, another solution for the coagulation problem may be needed, either through including explicit polarization or through strengthening protein–water interactions.