Long Time Molecular Dynamics for Enhanced Conformational Sampling in Biomolecular Systems

P. Minary, M. E. Tuckerman, and G. J. Martyna

Phys. Rev. Lett. 93, 150201 – Published 8 October 2004

Abstract

Although molecular dynamics methods are commonly used to drive biomolecular simulations, the technique provides insufficient sampling to impact studies of the 200-300 residue proteins of greatest interest. One severe limitation of molecular dynamics is that the integrators are restricted by resonance phenomena to small time steps $(Δ t < 8 f s)$ much slower then the time scales of important structural and solvent rearrangements. Here, a novel set of equations of motion and a reversible, resonance-free, integrator are designed which permit step sizes on the order of 100 fs to be used.

Received 20 April 2004

DOI:https://doi.org/10.1103/PhysRevLett.93.150201

Authors & Affiliations

P. Minary¹, M. E. Tuckerman^1,*, and G. J. Martyna²

¹Department of Chemistry, New York University, New York, New York 10003, USA
²IBM Physical Sciences Division, PO Box 218, Yorktown Heights, New York 10598, USA

^*Also at the Courant Institute of Mathematical Sciences, New York University, New York, New York 10003, USA

Article Text (Subscription Required)

Click to Expand

References (Subscription Required)

Click to Expand

Issue

Vol. 93, Iss. 15 — 8 October 2004

Reuse & Permissions

Access Options

Author publication services for translation and copyediting assistance advertisement

Physical Review Letters