• Corpus ID: 119228700

Free energy, friction, and mass profiles from short molecular dynamics trajectories

@article{PerezVilla2018FreeEF,
  title={Free energy, friction, and mass profiles from short molecular dynamics trajectories},
  author={Andrea P'erez-Villa and Fabio Pietrucci},
  journal={arXiv: Statistical Mechanics},
  year={2018}
}
We address the problem of constructing accurate mathematical models of the dynamics of molecular systems projected on a collective variable. To this aim we introduce an algorithm optimizing the parameters of a standard or generalized Langevin equation until the latter reproduces in a faithful way a set of molecular dynamics trajectories. In particular, using solvated proline dipeptide as a test case, we report evidence that ~100 short trajectories initiated at the top of a high barrier encode… 
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