PMID- 22612088
OWN - NLM
STAT- PubMed-not-MEDLINE
DCOM- 20120925
LR  - 20120522
IS  - 1089-7690 (Electronic)
IS  - 0021-9606 (Linking)
VI  - 136
IP  - 19
DP  - 2012 May 21
TI  - The multiscale coarse-graining method. X. Improved algorithms for constructing 
      coarse-grained potentials for molecular systems.
PG  - 194115
LID - 10.1063/1.4705420 [doi]
AB  - The multiscale coarse-graining (MS-CG) method uses simulation data for an 
      atomistic model of a system to construct a coarse-grained (CG) potential for a 
      coarse-grained model of the system. The CG potential is a variational 
      approximation for the true potential of mean force of the degrees of freedom 
      retained in the CG model. The variational calculation uses information about the 
      atomistic positions and forces in the simulation data. In principle, the 
      resulting MS-CG potential will be an accurate representation of the true CG 
      potential if the basis set for the variational calculation is complete enough and 
      the canonical distribution of atomistic states is well sampled by the data set. 
      In practice, atomistic configurations that have very high potential energy are 
      not sampled. As a result there usually is a region of CG configuration space that 
      is not sampled and about which the data set contains no information regarding the 
      gradient of the true potential. The MS-CG potential obtained from a variational 
      calculation will not necessarily be accurate in this unsampled region. A priori 
      considerations make it clear that the true CG potential of mean force must be 
      very large and positive in that region. To obtain an MS-CG potential whose 
      behavior in the sampled region is determined by the atomistic data set, and whose 
      behavior in the unsampled region is large and positive, it is necessary to 
      intervene in the variational calculation in some way. In this paper, we discuss 
      and compare two such methods of intervention, which have been used in previous 
      MS-CG calculations for dealing with nonbonded interactions. For the test systems 
      studied, the two methods give similar results and yield MS-CG potentials that are 
      limited in accuracy only by the incompleteness of the basis set and the 
      statistical error of associated with the set of atomistic configurations used. 
      The use of such methods is important for obtaining accurate CG potentials.
FAU - Das, Avisek
AU  - Das A
AD  - Department of Chemistry, Stanford University, Stanford, California 94305, USA.
FAU - Lu, Lanyuan
AU  - Lu L
FAU - Andersen, Hans C
AU  - Andersen HC
FAU - Voth, Gregory A
AU  - Voth GA
LA  - eng
PT  - Journal Article
PL  - United States
TA  - J Chem Phys
JT  - The Journal of chemical physics
JID - 0375360
EDAT- 2012/05/23 06:00
MHDA- 2012/05/23 06:01
CRDT- 2012/05/23 06:00
PHST- 2012/05/23 06:00 [entrez]
PHST- 2012/05/23 06:00 [pubmed]
PHST- 2012/05/23 06:01 [medline]
AID - 10.1063/1.4705420 [doi]
PST - ppublish
SO  - J Chem Phys. 2012 May 21;136(19):194115. doi: 10.1063/1.4705420.