Relaxation Estimation of RMSD in Molecular Dynamics Immunosimulations

نویسندگان

  • Wolfgang Schreiner
  • Rudolf Karch
  • Bernhard Knapp
  • Nevena Ilieva
چکیده

Molecular dynamics simulations have to be sufficiently long to draw reliable conclusions. However, no method exists to prove that a simulation has converged. We suggest the method of "lagged RMSD-analysis" as a tool to judge if an MD simulation has not yet run long enough. The analysis is based on RMSD values between pairs of configurations separated by variable time intervals Δt. Unless RMSD(Δt) has reached a stationary shape, the simulation has not yet converged.

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عنوان ژورنال:

دوره 2012  شماره 

صفحات  -

تاریخ انتشار 2012