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On the convergence of the conformational coordinates basis set obtained by the essential dynamics analysis of proteins' molecular dynamics simulations
Author(s) -
Amadei Andrea,
Ceruso Marc A.,
Di Nola Alfredo
Publication year - 1999
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/(sici)1097-0134(19990901)36:4<419::aid-prot5>3.0.co;2-u
Subject(s) - convergence (economics) , molecular dynamics , dynamics (music) , basis (linear algebra) , set (abstract data type) , nanosecond , statistical physics , range (aeronautics) , computer science , linear subspace , biological system , chemistry , computational chemistry , physics , mathematics , geometry , biology , engineering , aerospace engineering , laser , acoustics , optics , economics , programming language , economic growth
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. © 1999 Wiley‐Liss, Inc.