Dear users Please let me know some basic question. I am sorry if I am asking a silly question. a) While simulating a protein thermal unfolding at high temperature say 500K should I run position restraint dynamics at 500k or at 298K. I am doing 100ps position restraint dynamics at 500k. Am I right in doing so. b) While using Berendsen thermostat, how to select a value of tau_t and how does it affects simulation output. The same question for NoseHoover thermostat. c) After completing the 100ns simulation when I view the .xtc file in VMD I find that alpha helix of the protein is unfolded in very first frame collected at 10ps interval and reduced by trjconv at 50ps interval. Is it possible. If not then where I am wrong. I did Steepest descent minimization, then 100ps position restraint Dynamics at 500K and then 100ns full dynamics at 500k. msnayeem
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