Reconstructing potential energy functions from simulated force-induced unbinding processes

M. Balsera, S. Stepaniants, S. Izrailev, Y. Oono, K. Schulten

Research output: Contribution to journalArticlepeer-review

Abstract

One-dimensional stochastic models demonstrate that molecular dynamics simulations of a few nanoseconds can be used to reconstruct the essential features of the binding potential of macromolecules. This can be accomplished by inducing the unbinding with the help of external forces applied to the molecules and discounting the irreversible work performed on the system by these forces. The fluctuation-dissipation theorem sets a fundamental limit on the precision with which the binding potential can be reconstructed by this method. The uncertainty in the resulting potential is linearly proportional to the irreversible component of work performed on the system during the simulation. These results provide an a priori estimate of the energy barriers observable in molecular dynamics simulations.

Original languageEnglish (US)
Pages (from-to)1281-1287
Number of pages7
JournalBiophysical journal
Volume73
Issue number3
DOIs
StatePublished - Sep 1997

ASJC Scopus subject areas

  • Biophysics

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