Efficient free energy calculation of biomolecules from diffusion-biased molecular dynamics

Sadanand Singh, Chi-cheng Chiu, Juan J. De Pablo

Research output: Contribution to journalArticlepeer-review

10 Citations (Scopus)

Abstract

Recently proposed metadynamics techniques offer an effective means for improving sampling in simulations of complex systems, including polymers and biological macromolecules. One of the drawbacks of such methods has been the absence of well-defined or effective convergence criteria. A solution to this problem is considered here in which an optimal ensemble is introduced to minimize the travel time across the entire order parameter range of interest. The usefulness of the proposed approach is illustrated in the context of two systems consisting of biological molecules dissolved in water. The results presented in this work indicate that the proposed method is considerably faster than other existing algorithms for the study of these systems, and that the corresponding free energy that emerges from the simulations converges to the exact result.

Original languageEnglish
Pages (from-to)4657-4662
Number of pages6
JournalJournal of Chemical Theory and Computation
Volume8
Issue number11
DOIs
Publication statusPublished - 2012 Nov 13

All Science Journal Classification (ASJC) codes

  • Computer Science Applications
  • Physical and Theoretical Chemistry

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