PMID- 18601325
OWN - NLM
STAT- MEDLINE
DCOM- 20080828
LR  - 20240318
IS  - 1089-7690 (Electronic)
IS  - 0021-9606 (Print)
IS  - 0021-9606 (Linking)
VI  - 128
IP  - 24
DP  - 2008 Jun 28
TI  - The multiscale coarse-graining method. II. Numerical implementation for 
      coarse-grained molecular models.
PG  - 244115
LID - 10.1063/1.2938857 [doi]
LID - 244115
AB  - The multiscale coarse-graining (MS-CG) method [S. Izvekov and G. A. Voth, J. 
      Phys. Chem. B 109, 2469 (2005); J. Chem. Phys. 123, 134105 (2005)] employs a 
      variational principle to determine an interaction potential for a CG model from 
      simulations of an atomically detailed model of the same system. The companion 
      paper proved that, if no restrictions regarding the form of the CG interaction 
      potential are introduced and if the equilibrium distribution of the atomistic 
      model has been adequately sampled, then the MS-CG variational principle 
      determines the exact many-body potential of mean force (PMF) governing the 
      equilibrium distribution of CG sites generated by the atomistic model. In 
      practice, though, CG force fields are not completely flexible, but only include 
      particular types of interactions between CG sites, e.g., nonbonded forces between 
      pairs of sites. If the CG force field depends linearly on the force field 
      parameters, then the vector valued functions that relate the CG forces to these 
      parameters determine a set of basis vectors that span a vector subspace of CG 
      force fields. The companion paper introduced a distance metric for the vector 
      space of CG force fields and proved that the MS-CG variational principle 
      determines the CG force force field that is within that vector subspace and that 
      is closest to the force field determined by the many-body PMF. The present paper 
      applies the MS-CG variational principle for parametrizing molecular CG force 
      fields and derives a linear least squares problem for the parameter set 
      determining the optimal approximation to this many-body PMF. Linear systems of 
      equations for these CG force field parameters are derived and analyzed in terms 
      of equilibrium structural correlation functions. Numerical calculations for a 
      one-site CG model of methanol and a molecular CG model of the EMIM(+)NO(3) (-) 
      ionic liquid are provided to illustrate the method.
FAU - Noid, W G
AU  - Noid WG
AD  - Center for Biophysical Modeling and Simulation and Department of Chemistry, 
      University of Utah, Salt Lake City, Utah 84112-0850, USA.
FAU - Liu, Pu
AU  - Liu P
FAU - Wang, Yanting
AU  - Wang Y
FAU - Chu, Jhih-Wei
AU  - Chu JW
FAU - Ayton, Gary S
AU  - Ayton GS
FAU - Izvekov, Sergei
AU  - Izvekov S
FAU - Andersen, Hans C
AU  - Andersen HC
FAU - Voth, Gregory A
AU  - Voth GA
LA  - eng
GR  - F32 GM076839/GM/NIGMS NIH HHS/United States
PT  - Journal Article
PL  - United States
TA  - J Chem Phys
JT  - The Journal of chemical physics
JID - 0375360
RN  - 0 (Ionic Liquids)
RN  - Y4S76JWI15 (Methanol)
SB  - IM
CIN - J Chem Phys. 128:244114. PMID: 18601324
CIN - S. Izvekov and G. A. Voth, J. Phys. Chem. B 109, 2469 (2005);. PMID: 16851243
CIN - J. Chem. Phys. 123, 134105 (2005). PMID: 16223273
MH  - Computer Simulation
MH  - Ionic Liquids/chemistry
MH  - Methanol/chemistry
MH  - Models, Chemical
MH  - *Models, Molecular
MH  - Models, Statistical
MH  - Statistical Distributions
PMC - PMC2671180
EDAT- 2008/07/08 09:00
MHDA- 2008/08/30 09:00
PMCR- 2009/06/28
CRDT- 2008/07/08 09:00
PHST- 2008/07/08 09:00 [pubmed]
PHST- 2008/08/30 09:00 [medline]
PHST- 2008/07/08 09:00 [entrez]
PHST- 2009/06/28 00:00 [pmc-release]
AID - 507824JCP [pii]
AID - 10.1063/1.2938857 [doi]
PST - ppublish
SO  - J Chem Phys. 2008 Jun 28;128(24):244115. doi: 10.1063/1.2938857.