Abstract
ABSTRACTWe present a novel method to build a coarse-grained (CG) model based on the Mori-Zwanzig (MZ) formalism that reproduces kinetics. Our approach leads to the computation of a generalized Langevin equation (GLE), which includes the memory kernel and the fluctuation that are consistent with brute force molecular dynamics (MD) simulations. Our CG model based on the MZ formalism successfully reproduces kinetics, i.e. the distribution of first passage times (FPT) and velocity autocorrelation functions (VACF), for alanine dipeptide. In addition, we show that the memory part of the CG model of GLE is essential to reproduce kinetics. In other words, the Markovian model fails to reproduce brute force MD results, whereas the GLE model succeeds.
Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
