Coarse-Grained Force field

Model Nucleotide fragment Parameterization method Simulation method Reference 

MC-SYM Nucleotide cyclic motif ( 8 nt) Correct secondary structure Las Vegas [28] 

FARNA/ FARFAR 3 nt 7 dihedral an es sugar pucker Large ribosomal subunit Rosetta CG energy function Monte Carlo [21,22] 

RSIM 3 nt Doublet library from [31] Closed move Monte Carlo graph theory [29] 

BARNACLE 7 dihedral angles Dynamic Bayesian network Maximum likelihood estimation Monte Carlo [27] 

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Solvents (especially water) play a critical role in many biological processes or chemical reactions, so the development and improvement of coarse-grained force fields for solvents are essential to the CG modeling of biomolecules in solution. In addition, these small... 

Stark, A.C., Andrews, C.T., Elcock, A.H. Toward optimized potential functions for protein-protein interactions in aqueous solutions osmotic second virial coefficient calculations using the MARTINI coarse-grained force field. J. Chem. Theory Comput. 9, 4176 185... 

Monticelli, L., Kandasamy, S.K., Petiole, X., Larson, R.G., Tieleman, D.P., Marrink, S.-J. The MARTINI coarse-grained force field extension to proteins. J. Chem. Theory Comput. 4, 819-834 (2008)... 

These constrained MD methods rely on efficient solutions to the rigid-body EOM and on the use of atomistic, simplified atomistic (i.e., no intra-cluster valence or non-bond interactions) or coarse-grain force fields, discussed next. 

Molinero V, Goddard WA (2004) M3B a coarse grain force field for molecular simulations of malto-oligosaccharides and their water mixtures. J Phys Chem B 108(4) 1414—1427... 

All-atom force fields consider every atom as an individual interaction site, while united-atom force fields gather different atoms of a functional group into one interaction site, e.g., as is often done to model methyl or methylene groups. To describe chain-Uke polymers or proteins, coarse grained force fields are also employed, where the interaction sites usually represent a larger number of atoms. 

Classical Models Detailed-Atomistic and Coarse-Grained Force Fields for Multiscale Modeling of Electrolyte and Polyelectrolyte Solutions... 

Carbone P, Karimi-Varzaneh HA, Chem X, Miiller-Plathe F (2008) Transferability of coarse-grained force fields the polymer case. J Chem Phys 128 064904... 

Lopez CA, Rzepiela AJ, de Vries AH, Dijkhuizen L, Huenenberger PH, Marrink SJ (2009) Martini coarse-grained force field extension to carbohydrates. J Chem Theory Comput... 

MonticeUi L, Kandasamy SK, Periole X, et al The MARTINI coarse-grained force field extension to proteins,/ Chem Theory Comput 4 819—834, 2008. 

Wu Z, Cui Q, Yethiraj A A new coarse-grained force field for membrane-peptide simulations, J Chem Theory Comput 7 3793—3802, 2011. 

Daily, J.W. and Micci, M.M., Ionic velocities in an ionic liquid under high electric fields using all-atom and coarse-grained force field molecular dynamics, J. Chem. Phys. 131,... 

Shinoda W, DeVane R, Klein ML (2010) Zwitterionic lipid assemblies molecular dynamics studies of monolayers, bilayers, and vesicles using a new coarse grain force field. J Phys Chem B 114(20) 6836-6849... 

Nevertheless, supercapacitors necessitate very large simulation cells with explicit electrodes. This limits the number and the sizes of the systems that can be studied. A method which is often used to partially overcome this difficulty is to use coarse-grained force fields, i.e. to group several atoms together into a common interacting site, called grain. ... 

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