PMID- 26613319
OWN - NLM
STAT- PubMed-not-MEDLINE
DCOM- 20151201
LR  - 20151128
IS  - 1549-9618 (Print)
IS  - 1549-9618 (Linking)
VI  - 6
IP  - 3
DP  - 2010 Mar 9
TI  - Efficient, Regularized, and Scalable Algorithms for Multiscale Coarse-Graining.
PG  - 954-65
LID - 10.1021/ct900643r [doi]
AB  - The multiscale coarse-graining (MS-CG) method obtains CG interactions from 
      atomistic configurations, as demonstrated previously for a variety of soft matter 
      and biological systems. In this article, recent advances in MS-CG algorithms are 
      described, and a recently developed computer program MSCGFM for MS-CG 
      calculations is introduced. The algorithms enhance the efficiency and stability 
      of MS-CG computations, and these algorithms are incorporated into the MSCGFM 
      program. As a result of these efforts, MS-CG calculations on large scale systems 
      such as peptide and proteins can become tractable, and the numerical stability of 
      solutions for ill-posed MS-CG problems can be regularized efficiently. Various 
      parallelization strategies are also discussed.
FAU - Lu, Lanyuan
AU  - Lu L
AD  - Center for Biophysical Modeling and Simulation and Department of Chemistry, 
      University of Utah, Salt Lake City, Utah 84112-0850, and Department of Chemistry, 
      Stanford University, Stanford, California 94305.
FAU - Izvekov, Sergei
AU  - Izvekov S
AD  - Center for Biophysical Modeling and Simulation and Department of Chemistry, 
      University of Utah, Salt Lake City, Utah 84112-0850, and Department of Chemistry, 
      Stanford University, Stanford, California 94305.
FAU - Das, Avisek
AU  - Das A
AD  - Center for Biophysical Modeling and Simulation and Department of Chemistry, 
      University of Utah, Salt Lake City, Utah 84112-0850, and Department of Chemistry, 
      Stanford University, Stanford, California 94305.
FAU - Andersen, Hans C
AU  - Andersen HC
AD  - Center for Biophysical Modeling and Simulation and Department of Chemistry, 
      University of Utah, Salt Lake City, Utah 84112-0850, and Department of Chemistry, 
      Stanford University, Stanford, California 94305.
FAU - Voth, Gregory A
AU  - Voth GA
AD  - Center for Biophysical Modeling and Simulation and Department of Chemistry, 
      University of Utah, Salt Lake City, Utah 84112-0850, and Department of Chemistry, 
      Stanford University, Stanford, California 94305.
LA  - eng
PT  - Journal Article
DEP - 20100127
PL  - United States
TA  - J Chem Theory Comput
JT  - Journal of chemical theory and computation
JID - 101232704
EDAT- 2010/03/09 00:00
MHDA- 2010/03/09 00:01
CRDT- 2015/11/28 06:00
PHST- 2015/11/28 06:00 [entrez]
PHST- 2010/03/09 00:00 [pubmed]
PHST- 2010/03/09 00:01 [medline]
AID - 10.1021/ct900643r [doi]
PST - ppublish
SO  - J Chem Theory Comput. 2010 Mar 9;6(3):954-65. doi: 10.1021/ct900643r. Epub 2010 
      Jan 27.