Characterization of the structural ensembles of p53 TAD2 by molecular dynamics simulations with different force fields

Force Fields ◽

Structural Ensembles ◽

The conformations of p53 TAD2 in complexes and sampled in simulations with five force fields.

Structural Characterization of FeO–SiO2–V2O3 Slags Using Molecular Dynamics Simulations and FT-IR Spectroscopy

ISIJ International ◽

10.2355/isijinternational.isijint-2015-600 ◽

2016 ◽

Vol 56 (5) ◽

pp. 828-834 ◽

Cited By ~ 10

Author(s):

Zhen Zhang ◽

Bing Xie ◽

Wang Zhou ◽

Jiang Diao ◽

Hong-Yi Li

Keyword(s):

Molecular Dynamics ◽

Ir Spectroscopy ◽

Structural Characterization ◽

Ft Ir ◽

Dynamics Simulations ◽

Ft Ir Spectroscopy

Characterization of amorphous Si generated through classical molecular dynamics simulations

2017 Spanish Conference on Electron Devices (CDE) ◽

10.1109/cde.2017.7905213 ◽

2017 ◽

Author(s):

Ivan Santos ◽

Pedro Lopez ◽

Maria Aboy ◽

Luis A. Marques ◽

Lourdes Pelaz

Keyword(s):

Molecular Dynamics ◽

Classical Molecular Dynamics ◽

Amorphous Si ◽

Comparative Study of Force Fields for Molecular Dynamics Simulations of α-Glycine Crystal Growth from Solution

Crystal Growth & Design ◽

10.1021/cg100906s ◽

2010 ◽

Vol 10 (12) ◽

pp. 5146-5158 ◽

Cited By ~ 34

Author(s):

Daniel W. Cheong ◽

Yi Di Boon

Keyword(s):

Molecular Dynamics ◽

Crystal Growth ◽

Comparative Study ◽

Force Fields ◽

Growth From Solution ◽

Atomic scale characterization of interfacial water near an oxide surface using molecular dynamics simulations

Physical Chemistry Chemical Physics ◽

10.1039/c2cp42308a ◽

2012 ◽

Vol 14 (44) ◽

pp. 15593 ◽

Cited By ~ 21

Author(s):

Sanket A. Deshmukh ◽

Subramanian K. R. S. Sankaranarayanan

Keyword(s):

Molecular Dynamics ◽

Atomic Scale ◽

Oxide Surface ◽

Interfacial Water ◽

Scale Characterization ◽

How to strike a conformational balance in protein force fields for molecular dynamics simulations?

Wiley Interdisciplinary Reviews Computational Molecular Science ◽

10.1002/wcms.1578 ◽

2021 ◽

Author(s):

Wei Kang ◽

Fan Jiang ◽

Yun‐Dong Wu

Keyword(s):

Molecular Dynamics ◽

Force Fields ◽

Protein Force Fields ◽

Characterization of a Catalytic Ligand Bridging Metal Ions in Phosphodiesterases 4 and 5 by Molecular Dynamics Simulations and Hybrid Quantum Mechanical/Molecular Mechanical Calculations

Biophysical Journal ◽

10.1529/biophysj.106.086835 ◽

2006 ◽

Vol 91 (5) ◽

pp. 1858-1867 ◽

Cited By ~ 32

Author(s):

Ying Xiong ◽

Hai-Ting Lu ◽

Yongjian Li ◽

Guang-Fu Yang ◽

Chang-Guo Zhan

Keyword(s):

Molecular Dynamics ◽

Metal Ions ◽

Quantum Mechanical ◽

Experiment vs Force Fields: DNA Conformation from Molecular Dynamics Simulations

The Journal of Physical Chemistry B ◽

10.1021/jp971180a ◽

1997 ◽

Vol 101 (38) ◽

pp. 7361-7363 ◽

Cited By ~ 48

Author(s):

Michael Feig ◽

B. Montgomery Pettitt

Keyword(s):

Molecular Dynamics ◽

Force Fields ◽

Dna Conformation ◽

Effects of force fields on the conformational and dynamic properties of amyloid β(1-40) dimer explored by replica exchange molecular dynamics simulations

Proteins Structure Function and Bioinformatics ◽

10.1002/prot.25439 ◽

2017 ◽

Vol 86 (3) ◽

pp. 279-300 ◽

Cited By ~ 13

Author(s):

Charles R. Watts ◽

Andrew Gregory ◽

Cole Frisbie ◽

Sándor Lovas

Keyword(s):

Molecular Dynamics ◽

Force Fields ◽

Dynamic Properties ◽

Amyloid Β ◽

Replica Exchange ◽

Replica Exchange Molecular Dynamics ◽

Competition among Li+, Na+, K+, and Rb+Monovalent Ions for DNA in Molecular Dynamics Simulations Using the Additive CHARMM36 and Drude Polarizable Force Fields

The Journal of Physical Chemistry B ◽

10.1021/acs.jpcb.5b00683 ◽

2015 ◽

Vol 119 (12) ◽

pp. 4428-4440 ◽

Cited By ~ 52

Author(s):

Alexey Savelyev ◽

Alexander D. MacKerell

Keyword(s):

Molecular Dynamics ◽

Force Fields ◽

Polarizable Force Fields ◽

Monovalent Ions ◽

Structural characterization of the H2O/CCl4 liquid interface using molecular dynamics simulations

Surface and Colloid Science ◽

10.1007/b97086 ◽

2004 ◽

pp. 81-85 ◽

Cited By ~ 1

Author(s):

N. H. Moreira ◽

M. S. Skaf

Keyword(s):

Molecular Dynamics ◽

Structural Characterization ◽

Liquid Interface ◽