I am interested in the molecular dynamics simulation of a protein. The protein is homotetrameric and each chain contains more than 250 amino acids. I want to measure the changes in the protein at different pH. Would it be technically okay to simulate a single chain of the protein where all the chains would be identical?
Using a single chain as a minimum model system is not reasonable in this case because some solvent-exposed parts of the isolated chain would be shielded from the bulk solvent in the tetramer.
Thanks Martin Klavana for the response. It makes sense to me now. However, if you can, can you please suggest any alternative stategy to decrease the computation cost since I am very much limited to this resource.
It depends on what kind of simulation you are doing and what protein you are using. Without those information it is difficult to suggest to do something to reduce the computational cost.
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