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.
Rzepiela
Andrzej J
AJ
Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.
Schäfer
Lars V
LV
Goga
Nicolae
N
Risselada
H Jelger
HJ
De Vries
Alex H
AH
Marrink
Siewert J
SJ
D015060:1,2-Dipalmitoylphosphatidylcholine / Q000737:chemistry*; D000465:Algorithms; D002784:Cholesterol / Q000737:chemistry*; D008956:Models, Chemical; D056004:Molecular Dynamics Simulation
D015060:1,2-Dipalmitoylphosphatidylcholine; D002784:Cholesterol