hi..
We were working on the simulation of protein which has 3 chains (trimer) and each chain with a length of 80 amino acids. We have done the simulation for 5ns.We have observed a sudden shoot up in the RMS at 4ns so we continued simulating it to 10ns .The peak which started at 4ns extended till 8ns because of molecule breakage into monomer and dimer. we have also mutated some surface hydrophobic amino acid and dint observe shoot up in any of the mutated simulations. We have also observed the same shoot in the case of X ray crystallographic structure of template protein, when we did it for 10 ps simulation. We have done position Restraint Dynamics for 100 ps. What are the parameters i need to adjust during the simulation to get a stabilized modeled structure?? Does the PR parameters have any effect on simulation?? thanx Bhargavi
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