A new coarse grain model has been developed, which minimizes computational time by eliminating the unnecessary details of molecular calculations. We call this model COSMOS: COarSe grain MOlecular dynamics Simulation. This model speeds up calculations three to four orders of magnitude, allowing one to approach problems that were previously beyond the range of molecular dynamics. The PolyMedix coarse grain computational methods allow modeling on the time frame of several hundred µsecs, which is real time for many biological reactions. Previous molecular dynamics computational methods have generally been unable to model beyond approximately 10 nsec, regardless of how much computer hardware could be applied to the problem. The PolyMedix coarse-grain approach also increases accuracy by reducing modeling multiplicative errors. This model “summarizes” structures and represents atoms by chemical functionality in related groups rather than individually, as shown below:

Coarse Grain Molecular Dynamics Model:

PolyMedix used this approach to successfully design a series of antimicrobial commpounds, demonstrating that the model is effective, accurate, and very efficient in its use of computational power.

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