I wish to observe helix-coil transformation using MD simulation. What would be the minimum time scale for the simulation to observe such conformational transitions?
That depends ont he protein.peptide, but I believe that a reasonable timescale would be microseconds (http://www.ncbi.nlm.nih.gov/pubmed/11258895) or more.
Unless you want to force unfolding by providing a different environment (solvent or higher temperature) - see e.g. http://arxiv.org/ftp/arxiv/papers/1404/1404.5046.pdf or http://www.ncbi.nlm.nih.gov/pubmed/18339753 and many other papers: in such cases unfolding can be observed even in 20-50 nanoseconds.
if the temperature or solvent is changed how accurate wouldbthe result be and will be close to the in vivo behavior of the protein. This protein is bacterial cell division protein
Time hard, in orders, depending on which model of water used - explicit or implicit. In the implicit water may be enough even a few nanoseconds. For example http://www.biomolecular-modeling.com/Abalone/Protein-folding.html . But it certainly is a rarity.
I agree with the previous responses. Two additional pieces of advice, entropically it is easier to simulate unfolding than folding. So if you start from a helical conformation you can at least simulate the first events of unfolding, but it is difficult to simulate the first steps in the actual folding process. The second, you can accelerate the unfolding process by temperature but also by artificially stretching the helix along its axis in order to give the system a directed force in the unfolding direction.
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