Monte Carlo vs Molecular Dynamics for All-Atom Polypeptide Folding Simulations

Jakob P. Ulmschneider,* Martin B. Ulmschneider, and Alfredo Di Nola

Department of Chemistry, University of Rome "La Sapienza", Rome, Italy, and Department of Biochemistry, University of Oxford, Oxford, U.K.

Received: March 15, 2006

In Final Form: June 19, 2006

FULL TEXT

Abstract:

An efficient Monte Carlo (MC) algorithm including concerted rotations is directly compared to molecular dynamics (MD) in all-atom statistical mechanics folding simulations of small polypeptides. The previously reported algorithm "concerted rotations with flexible bond angles" (CRA) has been shown to successfully locate the native state of small polypeptides. In this study, the folding of three small polypeptides (trpzip2/H1/Trp-cage) is investigated using MC and MD, for a combined sampling time of ~10¹¹ MC configurations and 8 s, respectively. Both methods successfully locate the experimentally determined native states of the three systems, but they do so at different speed, with 2-2.5 times faster folding of the MC runs. The comparison reveals that thermodynamic and dynamic properties can reliably be obtained by both and that results from folding simulations do not depend on the algorithm used. Similar to previous comparisons of MC and MD, it is found that one MD integration step of 2 fs corresponds to one MC scan, revealing the good sampling of MC. The simplicity and efficiency of the MC method will enable its future use in folding studies involving larger systems and the combination with replica exchange algorithms.