Convergence of molecular dynamics simulations of membrane proteins

• DOI: 10.1002/prot.21308
• Publication Date: 2007-01-22T21:47:48Z
• Authors: Alan Grossfield; Scott E. Feller; Michael C. Pitman
• Keywords: Dynamics

Abstract The central question in evaluating almost any result from a molecular dynamics simulation is whether the calculation has converged. Unfortunately, assessing ergodicity of single trajectory very difficult to do. In this work, we assess sampling simulations membrane protein rhodopsin by comparing results 26 independent trajectories, each run for 100 ns. By examining principal components and cluster populations, show that rhodopsin's fluctuations are not well described ns dynamics, fully converged even individual loops. serve as reminder caution required when interpreting macromolecules. Proteins 2007. © 2007 Wiley‐Liss, Inc.