title: Reconstruction of atomistic details from coarse-grained structures.
abstract: 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.
authors.affiliation: Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.
authors.forename: Andrzej J
authors.initials: AJ
authors.lastname: Rzepiela
authors.forename: Lars V
authors.initials: LV
authors.lastname: Schäfer
authors.forename: Nicolae
authors.initials: N
authors.lastname: Goga
authors.forename: H Jelger
authors.initials: HJ
authors.lastname: Risselada
authors.forename: Alex H
authors.initials: AH
authors.lastname: De Vries
authors.forename: Siewert J
authors.initials: SJ
authors.lastname: Marrink
mesh_terms: D015060:1,2-Dipalmitoylphosphatidylcholine / Q000737:chemistry*; D000465:Algorithms; D002784:Cholesterol / Q000737:chemistry*; D008956:Models, Chemical; D056004:Molecular Dynamics Simulation
chemical_list: D015060:1,2-Dipalmitoylphosphatidylcholine; D002784:Cholesterol