Exploring Substrate Diffusion in Channels Using Biased Molecular Dynamics Simulations

  • James GumbartEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 914)


Substrate transport and diffusion through membrane-bound channels are processes that can span a range of time scales, with only the fastest ones being amenable to most atomic-scale equilibrium molecular dynamics (MD) simulations. However, the application of forces within a simulation can greatly accelerate diffusion processes, revealing important structural and energetic features of the channel. Here, we demonstrate the use of two methods for applying biases to a substrate in a simulation, using the ammonia/ammonium transporter AmtB as an example. The first method, steered MD, applies a constant force or velocity constraint to the substrate, permitting the exploration of potential substrate pathways and the barriers encountered, although typically far outside of equilibrium. On the other hand, the second method, adaptive biasing forces, is quasi-equilibrium, permitting the derivation of a potential of mean force, which characterizes the free energy of the substrate during transport.

Key words

Steered molecular dynamics Adaptive biasing forces Potential of mean force AmtB Ammonia/ammonium transport 



This work was supported by the National Institutes of Health (P41-RR005969). Simulations were run at the National Center for Supercomputing Applications (MCA93S028).


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Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  1. 1.Biosciences DivisionArgonne National LaboratoryArgonneUSA

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