Abstract

Modeling and enhanced sampling of molecular systems with smooth and nonlinear data-driven collective variables

Author (s): Hashemian, B, Millán, D. and Arroyo, M.
Journal: The Journal of Chemical Physics
Volume: 139, Number 21
Date: 2013

Abstract:
Collective variables (CVs) are low-dimensional representations of the state of a complex system, which help us rationalize molecular conformations and sample free energy landscapes with molecular dynamics simulations. Given their importance, there is need for systematic methods that effectively identify CVs for complex systems. In recent years, nonlinear manifold learning has shown its ability to automatically characterize molecular collective behavior. Unfortunately, these methods fail to provide a differentiable function mapping high-dimensional configurations to their low-dimensional representation, as required in enhanced sampling methods. We introduce a methodology that, starting from an ensemble representative of molecular flexibility, builds smooth and nonlinear data-driven collective variables (SandCV) from the output of nonlinear manifold learning algorithms. We demonstrate the method with a standard benchmark molecule, alanine dipeptide, and show how it can be non-intrusively combined with off-the-shelf enhanced sampling methods, here the adaptive biasing force method. We illustrate how enhanced sampling simulations with SandCV can explore regions that were poorly sampled in the original molecular ensemble. We further explore the transferability of SandCV from a simpler system, alanine dipeptide in vacuum, to a more complex system, alanine dipeptide in explicit water.

Featured Article of the issue and displayed on the Cover



     







Bibtex:
@article{JMR-MCAM:13,
  Author   = {Curiel, Jos{'e} L and Phaneendra, Sukumar  and Mu{\~n}oz, Jos\'e J},
  Title    = {Modelling of mixed damage on fibre-reinforced composite laminates subjected to low velocity impact},
  Fjournal = {International Journal of Damage Mechanics},
  Journal  = {Int. J. Dam. Mech.},
  Volume   = {22},
  Number   = {3},
  Pages    = {356--374},
  Year     = {2013}}