On the convergence of the conformational coordinates basis set obtained by the essential dynamics analysis of proteins' molecular dynamics simulations.
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.
Amadei
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Department of Chemistry, University of Rome "La Sapienza," Rome, Italy. amadei@degas.chem.uniromal.it
Ceruso
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Di Nola
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D000465:Algorithms; D001426:Bacterial Proteins; D003198:Computer Simulation; D003574:Cytochrome c Group / Q000737:chemistry; D004268:DNA-Binding Proteins / Q000737:chemistry; D007700:Kinetics; D008958:Models, Molecular; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D016008:Statistical Distributions; D013997:Time Factors
D001426:Bacterial Proteins; D003574:Cytochrome c Group; D004268:DNA-Binding Proteins; C116593:L-protein, Peptococcus magnus; D011506:Proteins