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Items: 1 to 20 of 111

1.

Adaptive multiscale molecular dynamics of macromolecular fluids.

Nielsen SO, Moore PB, Ensing B.

Phys Rev Lett. 2010 Dec 3;105(23):237802. Epub 2010 Dec 3.

PMID:
21231504
2.

Recent progress in adaptive multiscale molecular dynamics simulations of soft matter.

Nielsen SO, Bulo RE, Moore PB, Ensing B.

Phys Chem Chem Phys. 2010 Oct 21;12(39):12401-14. doi: 10.1039/c004111d. Epub 2010 Aug 24.

PMID:
20734007
3.

A macromolecule in a solvent: adaptive resolution molecular dynamics simulation.

Praprotnik M, Delle Site L, Kremer K.

J Chem Phys. 2007 Apr 7;126(13):134902.

PMID:
17430062
4.

The CUMULUS coarse graining method: transferable potentials for water and solutes.

van Hoof B, Markvoort AJ, van Santen RA, Hilbers PA.

J Phys Chem B. 2011 Aug 25;115(33):10001-12. doi: 10.1021/jp201975m. Epub 2011 Jul 28.

PMID:
21740053
5.

Hybrid simulations: combining atomistic and coarse-grained force fields using virtual sites.

Rzepiela AJ, Louhivuori M, Peter C, Marrink SJ.

Phys Chem Chem Phys. 2011 Jun 14;13(22):10437-48. doi: 10.1039/c0cp02981e. Epub 2011 Apr 15.

PMID:
21494747
6.

The multiscale coarse-graining method. VII. Free energy decomposition of coarse-grained effective potentials.

Lu L, Voth GA.

J Chem Phys. 2011 Jun 14;134(22):224107. doi: 10.1063/1.3599049.

PMID:
21682507
7.

Recent advances in transferable coarse-grained modeling of proteins.

Kar P, Feig M.

Adv Protein Chem Struct Biol. 2014;96:143-80. doi: 10.1016/bs.apcsb.2014.06.005. Epub 2014 Aug 24. Review.

PMID:
25443957
8.

Mixing MARTINI: electrostatic coupling in hybrid atomistic-coarse-grained biomolecular simulations.

Wassenaar TA, Ingólfsson HI, Priess M, Marrink SJ, Schäfer LV.

J Phys Chem B. 2013 Apr 4;117(13):3516-30. doi: 10.1021/jp311533p. Epub 2013 Mar 6.

9.

A hybrid all-atom/coarse grain model for multiscale simulations of DNA.

Machado MR, Dans PD, Pantano S.

Phys Chem Chem Phys. 2011 Oct 28;13(40):18134-44. doi: 10.1039/c1cp21248f. Epub 2011 Sep 19.

PMID:
21927740
10.

How to predict diffusion of medium-sized molecules in polymer matrices. From atomistic to coarse grain simulations.

Gautieri A, Vesentini S, Redaelli A.

J Mol Model. 2010 Dec;16(12):1845-51. doi: 10.1007/s00894-010-0687-7. Epub 2010 Mar 12.

PMID:
20224911
11.

The multiscale coarse-graining method: assessing its accuracy and introducing density dependent coarse-grain potentials.

Izvekov S, Chung PW, Rice BM.

J Chem Phys. 2010 Aug 14;133(6):064109. doi: 10.1063/1.3464776.

PMID:
20707563
12.

Adaptive resolution simulation of a biomolecule and its hydration shell: Structural and dynamical properties.

Fogarty AC, Potestio R, Kremer K.

J Chem Phys. 2015 May 21;142(19):195101. doi: 10.1063/1.4921347.

PMID:
26001481
13.

Molecular dynamics simulations of polyglutamine aggregation using solvent-free multiscale coarse-grained models.

Wang Y, Voth GA.

J Phys Chem B. 2010 Jul 8;114(26):8735-43. doi: 10.1021/jp1007768.

PMID:
20550147
14.

A coarse-grained model for polyethylene glycol polymer.

Wang Q, Keffer DJ, Nicholson DM.

J Chem Phys. 2011 Dec 7;135(21):214903. doi: 10.1063/1.3664623.

PMID:
22149813
15.

Effective force coarse-graining.

Wang Y, Noid WG, Liu P, Voth GA.

Phys Chem Chem Phys. 2009 Mar 28;11(12):2002-15. doi: 10.1039/b819182d. Epub 2009 Feb 12.

PMID:
19280011
16.

Adaptive resolution simulation of an atomistic protein in MARTINI water.

Zavadlav J, Melo MN, Marrink SJ, Praprotnik M.

J Chem Phys. 2014 Feb 7;140(5):054114. doi: 10.1063/1.4863329.

PMID:
24511929
17.

Macromolecular crowding: chemistry and physics meet biology (Ascona, Switzerland, 10-14 June 2012).

Foffi G, Pastore A, Piazza F, Temussi PA.

Phys Biol. 2013 Aug 2;10(4):040301. [Epub ahead of print]

PMID:
23912807
18.

Coarse-grained modeling for macromolecular chemistry.

Karimi-Varzaneh HA, Müller-Plathe F.

Top Curr Chem. 2012;307:295-321. doi: 10.1007/128_2010_122. Review.

PMID:
21360319
19.

Mixing coarse-grained and fine-grained water in molecular dynamics simulations of a single system.

Riniker S, van Gunsteren WF.

J Chem Phys. 2012 Jul 28;137(4):044120. doi: 10.1063/1.4739068.

PMID:
22852610
20.

Self-learning multiscale simulation for achieving high accuracy and high efficiency simultaneously.

Li W, Takada S.

J Chem Phys. 2009 Jun 7;130(21):214108. doi: 10.1063/1.3146922.

PMID:
19508057
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