Premium
Reconstruction of atomistic details from coarse‐grained structures
Author(s) -
Rzepiela Andrzej J.,
Schäfer Lars V.,
Goga Nicolae,
Risselada H. Jelger,
De Vries Alex H.,
Marrink Siewert J.
Publication year - 2010
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.21415
Subject(s) - molecular dynamics , simulated annealing , computer science , dipalmitoylphosphatidylcholine , statistical physics , chemical physics , materials science , algorithm , chemistry , physics , computational chemistry , membrane , phospholipid , biochemistry , phosphatidylcholine
We present an algorithm to reconstruct atomistic structures from their corresponding coarse‐grained (CG) representations and its implementation into the freely available molecular dynamics (MD) program package GROMACS. The central part of the algorithm is a simulated annealing MD simulation in which the CG and atomistic structures are coupled via restraints. A number of examples demonstrate the application of the reconstruction procedure to obtain low‐energy atomistic structural ensembles from their CG counterparts. We reconstructed individual molecules in vacuo (NCQ tripeptide, dipalmitoylphosphatidylcholine, and cholesterol), bulk water, and a WALP transmembrane peptide embedded in a solvated lipid bilayer. The first examples serve to optimize the parameters for the reconstruction procedure, whereas the latter examples illustrate the applicability to condensed‐phase biomolecular systems. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010