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Updated: Aug 21, 2026

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion
Published on: March 1, 2022
Long time molecular dynamics for enhanced conformational sampling in biomolecular systems
P Minary1, M E Tuckerman, G J Martyna
1Department of Chemistry, New York University, New York, New York 10003, USA.
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 (Delta t<8 fs) 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.
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