J Chem Inf Model - On the application of Good-Turing statistics to quantify convergence of biomolecular simulations.

Tópicos

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Resumo

Quantifying convergence and sufficient sampling of macromolecular molecular dynamics simulations is more often than not a source of controversy (and of various ad hoc solutions) in the field. Clearly, the only reasonable, consistent, and satisfying way to infer convergence (or otherwise) of a molecular dynamics trajectory must be based on probability theory. Ideally, the question we would wish to answer is the following: "What is the probability that a molecular configuration important for the analysis in hand has not yet been observed ?". Here we propose a method for answering a variant of this question by using the Good-Turing formalism for frequency estimation of unobserved species in a sample. Although several approaches may be followed in order to deal with the problem of discretizing the configurational space, for this work we use the classical RMSD matrix as a means to answering the following question: "What is the probability that a molecular configuration with an RMSD (from all other already observed configurations) higher than a given threshold has not actually been observed ?". We apply the proposed method to several different trajectories and show that the procedure appears to be both computationally stable and internally consistent. A free, open-source program implementing these ideas is immediately available for download via public repositories.

Resumo Limpo

quantifi converg suffici sampl macromolecular molecular dynam simul often sourc controversi various ad hoc solut field clear reason consist satisfi way infer converg otherwis molecular dynam trajectori must base probabl theori ideal question wish answer follow probabl molecular configur import analysi hand yet observ propos method answer variant question use goodtur formal frequenc estim unobserv speci sampl although sever approach may follow order deal problem discret configur space work use classic rmsd matrix mean answer follow question probabl molecular configur rmsd alreadi observ configur higher given threshold actual observ appli propos method sever differ trajectori show procedur appear comput stabl intern consist free opensourc program implement idea immedi avail download via public repositori

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