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Multiscale simulation of small peptides: Consistent conformational sampling in atomistic and coarse‐grained models
Author(s) -
Bezkorovaynaya Olga,
Lukyanov Alexander,
Kremer Kurt,
Peter Christine
Publication year - 2012
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.22915
Subject(s) - granularity , molecular dynamics , resolution (logic) , conformational ensembles , sampling (signal processing) , chemistry , statistical physics , biological system , computer science , computational chemistry , crystallography , physics , artificial intelligence , biology , filter (signal processing) , computer vision , operating system
A bottom–up coarse‐graining procedure for peptides in aqueous solution is presented, where the interactions in the coarse‐grained (CG) model are determined such that the CG peptide samples conformations according to a high‐resolution (atomistic) model. It is shown that important aspects of conformational sampling, such as correlated degrees of freedom (DOF) which play an important role in secondary structure formation, can be reproduced in the CG description. In some cases, microscopic structural/conformational details are lost in the coarse‐graining process. We show that these “lost” properties can be recovered in a backmapping procedure which reintroduces atomistic DOF into CG structures — as long as the overall conformational sampling of the molecule is correctly represented in the CG level of resolution. Thus, it is possible to link an existing all‐atom model of a biomolecular system with a CG description such that after inverse mapping one can recover structures at high resolution with the correctly sampled (according to the atomistic model) conformational properties. © 2012 Wiley Periodicals, Inc.