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Uncertainty in a Markov state model with missing states and rates: Application to a room temperature kinetic model obtained using high temperature molecular dynamics

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Title Uncertainty in a Markov state model with missing states and rates: Application to a room temperature kinetic model obtained using high temperature molecular dynamics
 
Creator CHATTERJEE, A
BHATTACHARYA, S
 
Subject REPLICA EXCHANGE SIMULATIONS
ALANINE DIPEPTIDE
CONFORMATIONAL TRANSITIONS
FOLDING SIMULATIONS
CHEMICAL-REACTIONS
INFREQUENT EVENTS
AQUEOUS-SOLUTION
NETWORK MODEL
TIME-SCALE
PROTEIN
 
Description Several studies in the past have generated Markov State Models (MSMs), i.e., kinetic models, of biomolecular systems by post-analyzing long standard molecular dynamics (MD) calculations at the temperature of interest and focusing on the maximally ergodic subset of states. Questions related to goodness of these models, namely, importance of the missing states and kinetic pathways, and the time for which the kinetic model is valid, are generally left unanswered. We show that similar questions arise when we generate a room-temperature MSM (denoted MSM-A) for solvated alanine dipeptide using state-constrained MD calculations at higher temperatures and Arrhenius relation - the main advantage of such a procedure being a speed-up of several thousand times over standard MD-based MSM building procedures. Bounds for rate constants calculated using probability theory from state-constrained MD at room temperature help validate MSM-A. However, bounds for pathways possibly missing in MSM-A show that alternate kinetic models exist that produce the same dynamical behaviour at short time scales as MSM-A but diverge later. Even in the worst case scenario, MSM-A is found to be valid longer than the time required to generate it. Concepts introduced here can be straightforwardly extended to other MSM building techniques. (C) 2015 AIP Publishing LLC.
 
Publisher AMER INST PHYSICS
 
Date 2016-01-15T07:46:44Z
2016-01-15T07:46:44Z
2015
 
Type Article
 
Identifier JOURNAL OF CHEMICAL PHYSICS, 143(11)
0021-9606
1089-7690
http://dx.doi.org/10.1063/1.4930976
http://dspace.library.iitb.ac.in/jspui/handle/100/18086
 
Language en