Extracting equilibrium and dynamic properties from molecular dynamics simulations
- Event time: 1:00pm
- Event date: 11th August 2014
- Speaker: Dr Antonia Mey (FU Berlin)
- Location: Room 2511, James Clerk Maxwell Building (JCMB) James Clerk Maxwell Building Peter Guthrie Tait Road Edinburgh EH9 3FD GB
Using molecular dynamics (MD) simulations to compute equilibrium and dynamic properties of complex systems has become a popular approach in recent years. The motivation behind these simulations is to be able to extract experimentally relevant observables, such as the folding rate of a protein, or the equilibrium population of the number of alpha-helices. I will give an introduction to Markov state models (MSM), an analysis tool for MD simulations that allows the extraction of the aforementioned equilibrium populations and transition rates from simulation data . In this context its usefulness as a tool for future force field improvements taking dynamic properties into account will be discussed. This will be achieved by analysing MSMs constructed from MD data of the same model systems (peptides), but simulated using different underlying MD force fields, resulting in a direct qualative comparision of the dynamics generated by commonly used force fields. Secondly, I will give an introduction how ideas behind MSMs in combination with multiple ensemble simulations can be used to derive a new class of equilibrium estimators -- the transition based reweighting analysis method (TRAM) -- that allow the estimation of equilibrium properties from simulations, carried out using enhanced sampling techniques such as umbrella sampling or temperature replica exchange simulations. I will discussed the expanded TRAM (xTRAM) estimator using exemplary systems of varying complexity, to demonstrate improved convergence (ranging from a two fold improvement to several orders of magnitude) over commonly used estimators, such as the multistate Bennett acceptance ratio (MBAR) .
[1 ]Prinz, J.-H. et al (2011) J.Chem. Phys. 134, p.174105  A.S.J.S Mey et al (2014) ArXiv:1407.0138  M.R. Shirts and J.D. Chodera (2008) J. Chem. Phys. 129 p. 124105
This is a weekly series of informal talks given primarily by members of the soft condensed matter and statistical mechanics groups, but is also open to members of other groups and external visitors. The aim of the series is to promote discussion and learning of various topics at a level suitable to the broad background of the group. Everyone is welcome to attend..