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. 1999 Sep 1;36(4):419-24.

On the convergence of the conformational coordinates basis set obtained by the essential dynamics analysis of proteins' molecular dynamics simulations

A Amadei  1 , M A Ceruso, A Di Nola
Affiliations
  • PMID: 10450083

On the convergence of the conformational coordinates basis set obtained by the essential dynamics analysis of proteins' molecular dynamics simulations

A Amadei et al. Proteins. .

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.

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