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On the convergence of the conformational coordinates basis set obtained by the essential dynamics analysis of
A Amadei1, M A Ceruso, A Di Nola
1Department of Chemistry, University of Rome "La Sapienza," Rome, Italy. amadei@degas.chem.uniromal.it
Proteins
|August 18, 1999
Abstract:
In this article we present a quantitative evaluation of the convergence of the conformational coordinates of proteins, obtained by the Essential Dynamics method. Using a detailed analysis of long molecular dynamics trajectories in combination with a statistical assessment of the significance of the measured convergence, we obtained that simulations of a few hundreds of picoseconds are in general sufficient to provide a stable and statistically reliable definition of the essential and near constraints subspaces, at least within the nanoseconds time range. Proteins 1999;36:419-424.