PMID- 24684663
OWN - NLM
STAT- PubMed-not-MEDLINE
DCOM- 20150511
LR  - 20140717
IS  - 1520-5207 (Electronic)
IS  - 1520-5207 (Linking)
VI  - 118
IP  - 28
DP  - 2014 Jul 17
TI  - Investigation of coarse-grained mappings via an iterative generalized 
      Yvon-Born-Green method.
PG  - 8295-312
LID - 10.1021/jp501694z [doi]
AB  - Low resolution coarse-grained (CG) models enable highly efficient simulations of 
      complex systems. The interactions in CG models are often iteratively refined over 
      multiple simulations until they reproduce the one-dimensional (1-D) distribution 
      functions, e.g., radial distribution functions (rdfs), of an all-atom (AA) model. 
      In contrast, the multiscale coarse-graining (MS-CG) method employs a generalized 
      Yvon-Born-Green (g-YBG) relation to determine CG potentials directly (i.e., 
      without iteration) from the correlations observed for the AA model. However, 
      MS-CG models do not necessarily reproduce the 1-D distribution functions of the 
      AA model. Consequently, recent studies have incorporated the g-YBG equation into 
      iterative methods for more accurately reproducing AA rdfs. In this work, we 
      consider a theoretical framework for an iterative g-YBG method. We numerically 
      demonstrate that the method robustly determines accurate models for both hexane 
      and also a more complex molecule, 3-hexylthiophene. By examining the MS-CG and 
      iterative g-YBG models for several distinct CG representations of both molecules, 
      we investigate the approximations of the MS-CG method and their sensitivity to 
      the CG mapping. More generally, we explicitly demonstrate that CG models often 
      reproduce 1-D distribution functions of AA models at the expense of distorting 
      the cross-correlations between the corresponding degrees of freedom. In 
      particular, CG models that accurately reproduce intramolecular 1-D distribution 
      functions may still provide a poor description of the molecular conformations 
      sampled by the AA model. We demonstrate a simple and predictive analysis for 
      determining CG mappings that promote an accurate description of these molecular 
      conformations.
FAU - Rudzinski, Joseph F
AU  - Rudzinski JF
AD  - Department of Chemistry, The Pennsylvania State University , University Park, 
      Pennsylvania 16802, United States.
FAU - Noid, William G
AU  - Noid WG
LA  - eng
PT  - Journal Article
DEP - 20140416
PL  - United States
TA  - J Phys Chem B
JT  - The journal of physical chemistry. B
JID - 101157530
EDAT- 2014/04/02 06:00
MHDA- 2014/04/02 06:01
CRDT- 2014/04/02 06:00
PHST- 2014/04/02 06:00 [entrez]
PHST- 2014/04/02 06:00 [pubmed]
PHST- 2014/04/02 06:01 [medline]
AID - 10.1021/jp501694z [doi]
PST - ppublish
SO  - J Phys Chem B. 2014 Jul 17;118(28):8295-312. doi: 10.1021/jp501694z. Epub 2014 
      Apr 16.