Renormalizing SMD: the renormalization approach and its use in long time simulations and accelerated PMF calculations of macromolecules.
Simulations of long time process in condensed phases, in general, and in biomolecules, in particular, present a major challenge that cannot be overcome at present by brute force molecular dynamics (MD) approaches. This work takes the renormalization method, intruded by us sometime ago, and establishes its reliability and potential in extending the time scale of molecular simulations. The validation involves a truncated gramicidin system in the gas phase. This system is small enough to allow for very long explicit simulations and sufficiently complex to present the physics of realistic ion channels. The renormalization approach is found to be reliable and arguably presents the first approach that allows one to exploit the otherwise problematic steered molecular dynamics (SMD) treatments in quantitative and meaningful studies. It is established that we can reproduce the long time behavior of large systems by using Langevin dynamics (LD) simulations of a renormalized implicit model. This is done without spending the enormous time needed to obtain such trajectories in the explicit system. The present study also provides a promising advance in accelerated evaluation of free energy barriers. This is done by adjusting the effective potential in the implicit model to reproduce the same passage time as that obtained in the explicit model under the influence of an external force. Here having a reasonable effective friction provides a way to extract the potential of mean force (PMF) without investing the time needed for regular PMF calculations. The renormalization approach, which is illustrated here in realistic calculations, is expected to provide a major help in studies of complex landscapes and in exploring long time dynamics of biomolecules.
Dryga
Anatoly
A
Department of Chemistry, University of Southern California, Los Angeles, California 90089-1062, USA.
Warshel
Arieh
A
D005740:Gases / Q000737:chemistry; D006096:Gramicidin / Q000737:chemistry; D056004:Molecular Dynamics Simulation
D005740:Gases; D006096:Gramicidin