Reconstruction of atomistic details from coarse‐grained structures

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