During my Material Studio molecular dynamics simulation of polymer surface-protein interactions, I've observed that proteins are escaping from the amorphous cell without adhering to the polymer surface. I would appreciate it if someone could kindly explain the reasons behind this unexpected behavior and how it can be better understood.Thank you in advance
To optimize the interaction between the protein and the surface, it is imperative to position the protein in close proximity to the surface. This proximity should take into account the van der Waals (vdW) interaction, which typically has a cutoff distance in the range of 12-14 Angstroms. It is crucial to verify the exact value of this cutoff distance before initiating the simulation. Placing the protein within this specified range is essential as positioning it beyond this limit increases the probability of little to no intra-interactions between the protein and the surface. While the vdW interactions are significant, it is also important to acknowledge the presence of electrostatic interactions in the system. Therefore, a meticulous examination of the system's structure is necessary to ensure that both vdW and electrostatic interactions are effectively balanced, contributing to the desired behavior in the simulation.
Proteins made up amino acids, the terminal amino acids have zwiter ion salt ,so that the reaction may be successed when the medium became basity with KOH solution
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