Monday, September 23, 2013

A new method for quantifying convergence of biomolecular simulations.

We have developed a new probabilistic method for quantifying convergence of molecular dynamics simulations. The essence of our method is the following : We treat the molecular dynamics trajectory as a finite sample of “molecular species” (clusters of similar structures) taken from an underlying distribution containing an unknown number of such molecular species. The observed frequencies of molecular species in the sample are calculated, and the Good-Turing formalism is applied to these frequencies allowing us to estimate the total probability of unseen (i.e. as yet unobserved) species. The result is the answer to 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?".

A paper containing a full description of the method is available from JCIM.

A program implementing the method is available via the github repository.

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