Rapid Free Energy Calculation of Peptide Self-Assembly by REMD Umbrella Sampling

MG Wolf, JA Jongejan, Jon Laman, SW de Leeuw

Research output: Contribution to journalArticleAcademicpeer-review

22 Citations (Scopus)

Abstract

We extend umbrella sampling with replica exchange steps to calculate free energies that are important in the self-assembly of peptides. This leads to a more than 10-fold speed up over conventional umbrella sampling, thereby providing a practical method to calculate these free-energy differences. This approach can also observe first-order phase transitions and pinpoint the location of the concomitant boundary. When conformational changes are involved, this method can handle peptides up to similar to 7 residues, providing a rapid and accurate assessment of the thermodynamic properties of model systems, and can thus be used to answer fundamental questions about peptide self-assembly. When no major conformational changes are involved, we expect the size limit to be equal to that of standard molecular dynamics.
Original languageUndefined/Unknown
Pages (from-to)13493-13498
Number of pages6
JournalJournal of Physical Chemistry B
Volume112
Issue number43
DOIs
Publication statusPublished - 2008

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