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Normal Mode AnalysisTable of contentsNormal procedure with GROMACSIn Normal Mode Analysis (NMA), calculations are run in order to study the underlying, large-scale functional motions of a macromolecule, typically a protein. The calculations require very thorough energy minimization and calculation of a Hessian matrix. In general, both for final-stage energy minimization (with L-BFGS) and actual normal mode analysis you can use a setup with
It is imperative that you use the
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