PMID- 22292916
OWN - NLM
STAT- PubMed-not-MEDLINE
DCOM- 20121127
LR  - 20120726
IS  - 1520-5207 (Electronic)
IS  - 1520-5207 (Linking)
VI  - 116
IP  - 29
DP  - 2012 Jul 26
TI  - Coarse-grained modeling of simple molecules at different resolutions in the 
      absence of good sampling.
PG  - 8337-49
LID - 10.1021/jp2097263 [doi]
AB  - Many problems of interest in modern science originate from the complex network of 
      interactions of different molecular structures, each possessing its own typical 
      length and time scale of relevance. In such materials, nontrivial properties 
      emerge from the different length and time scales involved that could not be 
      predicted from the properties of each individual subunit taken alone. A solution 
      to the formidable theoretical and computational issues raised by these systems 
      involves coarse-graining, a procedure in which multiple atoms are grouped into a 
      few interaction sites. The coarse-grained approach aims at constructing an 
      effective Hamiltonian from available information about the system and then using 
      this Hamiltonian to investigate the behavior of the system on the length and time 
      scales of interest. In this paper, we aim at determining how far we can 
      coarse-grain a system using only the commonly used pairwise, spherically 
      symmetric potentials, as well as assessing the impact of poor initial sampling on 
      the quality of the resulting coarse-grained model. Coarse-graining is performed 
      following the multiscale coarse-graining (MS-CG) methodology, and we use as a 
      model system the N-methylacetamide (NMA) molecule, a simple representation of a 
      peptide bond, which can adopt two conformations, cis and trans. Our simulations 
      reveal that as the coarse-graining becomes more aggressive multibody effects 
      start to emerge and that the initial sampling of conformations can adversely bias 
      the model in the case of heavy coarse-graining.
FAU - Larini, Luca
AU  - Larini L
AD  - Department of Chemistry and Biochemistry and of Physics, University of 
      California, Santa Barbara, Santa Barbara, California 93106, United States.
FAU - Shea, Joan-Emma
AU  - Shea JE
LA  - eng
PT  - Journal Article
DEP - 20120302
PL  - United States
TA  - J Phys Chem B
JT  - The journal of physical chemistry. B
JID - 101157530
EDAT- 2012/02/02 06:00
MHDA- 2012/02/02 06:01
CRDT- 2012/02/02 06:00
PHST- 2012/02/02 06:00 [entrez]
PHST- 2012/02/02 06:00 [pubmed]
PHST- 2012/02/02 06:01 [medline]
AID - 10.1021/jp2097263 [doi]
PST - ppublish
SO  - J Phys Chem B. 2012 Jul 26;116(29):8337-49. doi: 10.1021/jp2097263. Epub 2012 Mar 
      2.