Expectation maximized molecular dynamics: Toward efficient learning of rarely sampled features in free energy surfaces from unbiased simulations

Pallab Dutta; Neelanjana Sengupta

doi:10.1063/5.0021910

Expectation maximized molecular dynamics: Toward efficient learning of rarely sampled features in free energy surfaces from unbiased simulations

The Journal of Chemical Physics ◽

10.1063/5.0021910 ◽

2020 ◽

Vol 153 (15) ◽

pp. 154104

Author(s):

Pallab Dutta ◽

Neelanjana Sengupta

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Efficient Learning ◽

Energy Surfaces

Download Full-text

Potential energy and free energy surfaces of the formic acid dimer: Correlated ab initio calculations and molecular dynamics simulationsElectronic supplementary information (ESI) available: Optimised geometries of the structures in Tables 1 and 2. See http://www.rsc.org/suppdata/cp/b1/b110872g/

Physical Chemistry Chemical Physics ◽

10.1039/b110872g ◽

2002 ◽

Vol 4 (11) ◽

pp. 2119-2122 ◽

Cited By ~ 39

Author(s):

Jana Chocholoušová ◽

Jaroslav Vacek ◽

Pavel Hobza

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Potential Energy ◽

Formic Acid ◽

Ab Initio Calculations ◽

Ab Initio ◽

Supplementary Information ◽

Energy Surfaces

Download Full-text

Simulated annealing on free energy surfaces by a combined molecular dynamics and Monte Carlo approach

The Journal of Physical Chemistry ◽

10.1021/j100107a015 ◽

1993 ◽

Vol 97 (5) ◽

pp. 1069-1073 ◽

Cited By ~ 42

Author(s):

Bruce Tidor

Keyword(s):

Molecular Dynamics ◽

Monte Carlo ◽

Free Energy ◽

Simulated Annealing ◽

Monte Carlo Approach ◽

Energy Surfaces

Download Full-text

Potential Energy and Free Energy Surfaces of All Ten Canonical and Methylated Nucleic Acid Base Pairs: Molecular Dynamics and Quantum Chemical ab Initio Studies

The Journal of Physical Chemistry B ◽

10.1021/jp0104886 ◽

2001 ◽

Vol 105 (24) ◽

pp. 5804-5817 ◽

Cited By ~ 59

Author(s):

Martin Kabeláč ◽

Pavel Hobza

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Nucleic Acid ◽

Potential Energy ◽

Ab Initio ◽

Quantum Chemical ◽

Acid Base ◽

Base Pairs ◽

Nucleic Acid Base ◽

Energy Surfaces

Download Full-text

ORAC: A molecular dynamics simulation program to explore free energy surfaces in biomolecular systems at the atomistic level

Journal of Computational Chemistry ◽

10.1002/jcc.21388 ◽

2009 ◽

pp. NA-NA ◽

Cited By ~ 18

Author(s):

Simone Marsili ◽

Giorgio Federico Signorini ◽

Riccardo Chelli ◽

Massimo Marchi ◽

Piero Procacci

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulation ◽

Dynamics Simulation ◽

Simulation Program ◽

Biomolecular Systems ◽

Energy Surfaces

Download Full-text

Free energy surfaces of β-hairpin and α-helical peptides generated by replica exchange molecular dynamics with the AGBNP implicit solvent model

Proteins Structure Function and Bioinformatics ◽

10.1002/prot.20104 ◽

2004 ◽

Vol 56 (2) ◽

pp. 310-321 ◽

Cited By ~ 97

Author(s):

Anthony K. Felts ◽

Yuichi Harano ◽

Emilio Gallicchio ◽

Ronald M. Levy

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Replica Exchange ◽

Implicit Solvent ◽

Helical Peptides ◽

Replica Exchange Molecular Dynamics ◽

Implicit Solvent Model ◽

Solvent Model ◽

Energy Surfaces

Download Full-text

Efficient computation of free energy surfaces of chemical reactions using ab initio molecular dynamics with hybrid functionals and plane waves

Journal of Computational Chemistry ◽

10.1002/jcc.26222 ◽

2020 ◽

Vol 41 (19) ◽

pp. 1790-1797 ◽

Cited By ~ 1

Author(s):

Sagarmoy Mandal ◽

Nisanth N. Nair

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Ab Initio ◽

Chemical Reactions ◽

Plane Waves ◽

Ab Initio Molecular Dynamics ◽

Efficient Computation ◽

Hybrid Functionals ◽

Energy Surfaces

Download Full-text

Realistic Quantitative Descriptions of Electron Transfer Reactions: Diabatic Free-Energy Surfaces from First-Principles Molecular Dynamics

Physical Review Letters ◽

10.1103/physrevlett.97.028303 ◽

2006 ◽

Vol 97 (2) ◽

Cited By ~ 50

Author(s):

P. H.-L. Sit ◽

Matteo Cococcioni ◽

Nicola Marzari

Keyword(s):

Molecular Dynamics ◽

Electron Transfer ◽

Free Energy ◽

First Principles ◽

Transfer Reactions ◽

Electron Transfer Reactions ◽

Energy Surfaces ◽

First Principles Molecular Dynamics

Download Full-text

Free energy surfaces of miniproteins with a ββα motif: Replica exchange molecular dynamics simulation with an implicit solvation model

Proteins Structure Function and Bioinformatics ◽

10.1002/prot.20771 ◽

2005 ◽

Vol 62 (3) ◽

pp. 663-671 ◽

Cited By ~ 30

Author(s):

Soonmin Jang ◽

Eunae Kim ◽

Youngshang Pak

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulation ◽

Dynamics Simulation ◽

Replica Exchange ◽

Implicit Solvation ◽

Solvation Model ◽

Replica Exchange Molecular Dynamics ◽

Implicit Solvation Model ◽

Energy Surfaces

Download Full-text

Effects of hydration on the protonation state of a lysine analog crossing a phospholipid bilayer – insights from molecular dynamics and free-energy calculations

Physical Chemistry Chemical Physics ◽

10.1039/c8cp00312b ◽

2018 ◽

Vol 20 (14) ◽

pp. 9101-9107 ◽

Cited By ~ 5

Author(s):

Daniel Bonhenry ◽

François Dehez ◽

Mounir Tarek

Keyword(s):

Molecular Dynamics ◽

Amino Acids ◽

Free Energy ◽

Lipid Bilayers ◽

Free Energy Calculations ◽

Phospholipid Bilayer ◽

Protonation State ◽

Energy Calculations ◽

Energy Surfaces

Protonation states of amino acids crossing lipid bilayers from multidimensional free energy surfaces.

Download Full-text

Potential Energy and Free Energy Surfaces of Floppy Systems. Ab initio Calculations and Molecular Dynamics Simulations

Theoretical and Computational Chemistry - Molecular Dynamics - From Classical to Quantum Methods ◽

10.1016/s1380-7323(99)80053-3 ◽

1999 ◽

pp. 829-857 ◽

Cited By ~ 2

Author(s):

Pavel Hobza

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Potential Energy ◽

Ab Initio Calculations ◽

Ab Initio ◽

Molecular Dynamics Simulations ◽

Dynamics Simulations ◽

Energy Surfaces

Download Full-text