Reconstruction of atomistic details from coarse-grained structures

Citation (APA 7)

Rzepiela, A. J., Schäfer, L. V., Goga, N., Risselada, H. J., De Vries, A. H., & Marrink, S. J. (2010). Reconstruction of atomistic details from coarse‐grained structures. Journal of computational chemistry, 31(6), 1333-1343.

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.