Format
Sort by
Items per page

Send to

Choose Destination

Links from PubMed

Items: 1 to 20 of 85

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.

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
5.

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
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
7.
8.

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
9.

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
10.

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
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.

Assessing the Quality of the OPEP Coarse-Grained Force Field.

Barducci A, Bonomi M, Derreumaux P.

J Chem Theory Comput. 2011 Jun 14;7(6):1928-34. doi: 10.1021/ct100646f. Epub 2011 May 19.

PMID:
26596453
13.

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
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.

Ion-selective interactions of biologically relevant inorganic ions with alanine zwitterion: a 3D-RISM study.

Fedotova MV, Dmitrieva OA.

Amino Acids. 2015 May;47(5):1015-23. doi: 10.1007/s00726-015-1930-4. Epub 2015 Feb 8.

PMID:
25663287
16.

Energy landscapes and properties of biomolecules.

Wales DJ.

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

PMID:
16280625
17.

Salting out of methane by sodium chloride: A scaled particle theory study.

Graziano G.

J Chem Phys. 2008 Aug 28;129(8):084506. doi: 10.1063/1.2972979.

PMID:
19044834
18.

Specific interactions of sodium salts with alanine dipeptide and tetrapeptide in water: insights from molecular dynamics.

Ioannou F, Archontis G, Leontidis E.

J Phys Chem B. 2011 Nov 17;115(45):13389-400. doi: 10.1021/jp207068m. Epub 2011 Oct 24.

PMID:
21978277
19.

Energy landscapes and global thermodynamics for alanine peptides.

Somani S, Wales DJ.

J Chem Phys. 2013 Sep 28;139(12):121909. doi: 10.1063/1.4813627.

PMID:
24089721
20.

Free Energy Landscapes of Alanine Oligopeptides in Rigid-Body and Hybrid Water Models.

Nayar D, Chakravarty C.

J Phys Chem B. 2015 Aug 27;119(34):11106-20. doi: 10.1021/acs.jpcb.5b02937. Epub 2015 Jul 16.

PMID:
26132437

Supplemental Content

Support Center