I am trying to strudy force induced unfolding of protein by constant force SMD Simulation using NAMD. I have used GBIS, because the water model is not possible. I see that my protein completely unfolds within 2ns of simulation when 80pN force is applied. I am not sure if my run is correct ?
You could analyze results in different ways: for example calculate end-to-end distance versus simulation time for different applied forces (80pN and higher than that or slightly lower; there are published papers that report applied forces up to 1000 pN; of course with increasing force protein unfolds faster) . Other analysis you can perform is the number of H-bonds versus time and for different applied forces, or the area exposed hydrophobic residues versus extension of protein, and extension versus applied force.
You should also look for experimental data of AFM about your system if exists any and compare your results with.
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