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Items: 1 to 20 of 91

1.

Escaping free-energy minima.

Laio A, Parrinello M.

Proc Natl Acad Sci U S A. 2002 Oct 1;99(20):12562-6. Epub 2002 Sep 23.

2.

Metadynamics in essential coordinates: free energy simulation of conformational changes.

Spiwok V, Lipovová P, Králová B.

J Phys Chem B. 2007 Mar 29;111(12):3073-6. Epub 2007 Mar 6.

PMID:
17388445
3.

Metadynamics as a tool for mapping the conformational and free-energy space of peptides--the alanine dipeptide case study.

Vymetal J, Vondrásek J.

J Phys Chem B. 2010 Apr 29;114(16):5632-42. doi: 10.1021/jp100950w.

PMID:
20361773
4.

Coarse master equation from Bayesian analysis of replica molecular dynamics simulations.

Sriraman S, Kevrekidis IG, Hummer G.

J Phys Chem B. 2005 Apr 14;109(14):6479-84.

PMID:
16851726
5.

Molecular dynamics studies on the thermodynamics of supercooled sodium chloride aqueous solution at different concentrations.

Corradini D, Gallo P, Rovere M.

J Phys Condens Matter. 2010 Jul 21;22(28):284104. doi: 10.1088/0953-8984/22/28/284104. Epub 2010 Jun 21.

PMID:
21399276
6.

Efficient and direct generation of multidimensional free energy surfaces via adiabatic dynamics without coordinate transformations.

Abrams JB, Tuckerman ME.

J Phys Chem B. 2008 Dec 11;112(49):15742-57. doi: 10.1021/jp805039u.

PMID:
19367870
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9.

Accelerated molecular dynamics: a promising and efficient simulation method for biomolecules.

Hamelberg D, Mongan J, McCammon JA.

J Chem Phys. 2004 Jun 22;120(24):11919-29.

PMID:
15268227
10.

Continuous metadynamics in essential coordinates as a tool for free energy modelling of conformational changes.

Spiwok V, Králová B, Tvaroska I.

J Mol Model. 2008 Nov;14(11):995-1002. doi: 10.1007/s00894-008-0343-7. Epub 2008 Jul 17.

PMID:
18633653
11.

Computing accurate potentials of mean force in electrolyte solutions with the generalized gradient-augmented harmonic Fourier beads method.

Khavrutskii IV, Dzubiella J, McCammon JA.

J Chem Phys. 2008 Jan 28;128(4):044106. doi: 10.1063/1.2825620.

PMID:
18247929
12.

Dissociation of NaCl in water from ab initio molecular dynamics simulations.

Timko J, Bucher D, Kuyucak S.

J Chem Phys. 2010 Mar 21;132(11):114510. doi: 10.1063/1.3360310.

PMID:
20331308
13.

Coarse-grained ions without charges: reproducing the solvation structure of NaCl in water using short-ranged potentials.

DeMille RC, Molinero V.

J Chem Phys. 2009 Jul 21;131(3):034107. doi: 10.1063/1.3170982.

PMID:
19624181
14.

Molecular renormalization group coarse-graining of electrolyte solutions: application to aqueous NaCl and KCl.

Savelyev A, Papoian GA.

J Phys Chem B. 2009 Jun 4;113(22):7785-93. doi: 10.1021/jp9005058.

PMID:
19425537
15.
16.

Exploring the free-energy landscape of a short peptide using an average force.

Chipot C, Hénin J.

J Chem Phys. 2005 Dec 22;123(24):244906.

PMID:
16396572
17.

Energy landscapes and properties of biomolecules.

Wales DJ.

Phys Biol. 2005 Nov 9;2(4):S86-93.

PMID:
16280625
18.

On the Use of Accelerated Molecular Dynamics to Enhance Configurational Sampling in Ab Initio Simulations.

Bucher D, Pierce LC, McCammon JA, Markwick PR.

J Chem Theory Comput. 2011 Apr 12;7(4):890-897. Epub 2011 Mar 4.

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20.

Mapping potential energy surfaces.

Wu Y, Schmitt JD, Car R.

J Chem Phys. 2004 Jul 15;121(3):1193-200.

PMID:
15260660
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