On the convergence of the conformational coordinates basis set obtained by the essential dynamics analysis of proteins' molecular dynamics simulations
Amadei A, Ceruso MA, Di Nola A
PROTEINS-STRUCTURE FUNCTION AND GENETICS
36 (4): 419-424 SEP 1 1999

FULL TEXT

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. (C) 1999 Wiley-Liss, Inc.

Author Keywords:

essential dynamics, molecular dynamics, conformational fluctuations

Addresses:

Amadei A, Univ Rome La Sapienza, Dept Chem, POB 34 Roma 62,Ple Aldo Moro 5, I-00185 Rome, Italy
Univ Rome La Sapienza, Dept Chem, I-00185 Rome, Italy