PMID- 29227668
OWN - NLM
STAT- PubMed-not-MEDLINE
DCOM- 20180502
LR  - 20180502
IS  - 1520-5207 (Electronic)
IS  - 1520-5207 (Linking)
VI  - 122
IP  - 13
DP  - 2018 Apr 5
TI  - BOCS: Bottom-up Open-source Coarse-graining Software.
PG  - 3363-3377
LID - 10.1021/acs.jpcb.7b09993 [doi]
AB  - We present the BOCS toolkit as a suite of open source software tools for 
      parametrizing bottom-up coarse-grained (CG) models to accurately reproduce 
      structural and thermodynamic properties of high-resolution models. The BOCS 
      toolkit complements available software packages by providing robust 
      implementations of both the multiscale coarse-graining (MS-CG) force-matching 
      method and also the generalized-Yvon-Born-Green (g-YBG) method. The g-YBG method 
      allows one to analyze and to calculate MS-CG potentials in terms of structural 
      correlations. Additionally, the BOCS toolkit implements an extended ensemble 
      framework for optimizing the transferability of bottom-up potentials, as well as 
      a self-consistent pressure-matching method for accurately modeling the pressure 
      equation of state for homogeneous systems. We illustrate these capabilities by 
      parametrizing transferable potentials for CG models that accurately model the 
      structure, pressure, and compressibility of liquid alkane systems and by 
      quantifying the role of many-body correlations in determining the calculated pair 
      potential for a one-site CG model of liquid methanol.
FAU - Dunn, Nicholas J H
AU  - Dunn NJH
AD  - Department of Chemistry , The Pennsylvania State University , University Park , 
      Pennsylvania 16802 , United States.
FAU - Lebold, Kathryn M
AU  - Lebold KM
AD  - Department of Chemistry , The Pennsylvania State University , University Park , 
      Pennsylvania 16802 , United States.
FAU - DeLyser, Michael R
AU  - DeLyser MR
AD  - Department of Chemistry , The Pennsylvania State University , University Park , 
      Pennsylvania 16802 , United States.
FAU - Rudzinski, Joseph F
AU  - Rudzinski JF
AUID- ORCID: 0000-0003-3403-640X
AD  - Department of Chemistry , The Pennsylvania State University , University Park , 
      Pennsylvania 16802 , United States.
FAU - Noid, W G
AU  - Noid WG
AUID- ORCID: 0000-0001-9675-8489
AD  - Department of Chemistry , The Pennsylvania State University , University Park , 
      Pennsylvania 16802 , United States.
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
PT  - Research Support, U.S. Gov't, Non-P.H.S.
DEP - 20180112
PL  - United States
TA  - J Phys Chem B
JT  - The journal of physical chemistry. B
JID - 101157530
EDAT- 2017/12/12 06:00
MHDA- 2017/12/12 06:01
CRDT- 2017/12/12 06:00
PHST- 2017/12/12 06:00 [pubmed]
PHST- 2017/12/12 06:01 [medline]
PHST- 2017/12/12 06:00 [entrez]
AID - 10.1021/acs.jpcb.7b09993 [doi]
PST - ppublish
SO  - J Phys Chem B. 2018 Apr 5;122(13):3363-3377. doi: 10.1021/acs.jpcb.7b09993. Epub 
      2018 Jan 12.