Molecular Dynamic Simulations of Environment and Sequence Dependent DNA Conformations: The Development of the BMS Nucleic Acid Force Field and Comparison with Experimental Results

1998 ◽  
Vol 16 (3) ◽  
pp. 487-509 ◽  
Author(s):  
David R. Langley
Keyword(s):  
Nucleic Acid ◽  
Force Field ◽  
Molecular Dynamic ◽  
Experimental Results ◽  
Molecular Dynamic Simulations ◽  
Dynamic Simulations ◽  
Sequence Dependent ◽  
Dna Conformations

scholarly journals Molecular dynamic simulations on TKX-50/HMX cocrystal

RSC Advances ◽  
2017 ◽  
Vol 7 (11) ◽  
pp. 6795-6799 ◽  
Author(s):  
Shuling Xiong ◽  
Shusen Chen ◽  
Shaohua Jin ◽  
Zhe Zhang ◽  
Yan Zhang ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Molecular Dynamics Simulations ◽  
Molecular Dynamic ◽  
Molecular Dynamic Simulations ◽  
Dynamic Simulations ◽  
Dynamics Simulations

TKX-50/HMX cocrystal model was established and calculated using PCFF force field by molecular dynamics simulations.

Determination of the Structures of Uranyl-Tri-n-butyl-Phosphate Aggregates by Coupling Experimental Results with Molecular Dynamic Simulations

2017 ◽  
Vol 23 (65) ◽  
pp. 16660-16670 ◽  
Author(s):  
Phillipe Guilbaud ◽  
Laurence Berthon ◽  
Wilfried Louisfrema ◽  
Olivier Diat ◽  
Nicole Zorz
Keyword(s):  
Molecular Dynamic ◽  
Experimental Results ◽  
Molecular Dynamic Simulations ◽  
Dynamic Simulations

scholarly journals STRUCTURAL CHARACTERISTICS OF 8-CROWN-6 MOLECULE IN METHANOL AND ACETONITRILE

2018 ◽  
Vol 59 (4) ◽  
pp. 22 ◽  
Author(s):  
Irina A. Kuz'mina ◽  
Tatiana R. Usacheva ◽  
Mariya A. Volkova ◽  
Natalia V. Belova ◽  
Valentin A. Sharnin
Keyword(s):  
Hydrogen Bonds ◽  
Force Field ◽  
Molecular Dynamic ◽  
Quantum Chemical ◽  
Structural Characteristics ◽  
Molecular Dynamic Simulations ◽  
Dynamic Simulations ◽  
Stable Conformation ◽  
Atomic Force ◽  
Basic Set

Quantum-chemical calculations of stable conformation of the molecule of 18-crown-6 ether (18C6) were carried for its free state in methanol (MeOH) and acetonitrile (AN) using GAUSSIAN 03 program. The DFT version and cc-pVTZ basic set was used. The values of mean lifetimes of hydrogen bonds between the methanol molecules as well as between 18C6 and methanol in MeOH-MeOH и 18C6-{MeOH-MeOH} systems were calculated by molecular dynamic simulations in NVT- ensemble applying GROMACS 4.5.4 software for OPLS-AA full-atomic force field .

Ramachandran-type plots for glycosidic linkages: Examples from molecular dynamic simulations using the Glycam06 force field

2009 ◽  
Vol 30 (6) ◽  
pp. 910-921 ◽  
Author(s):  
Amanda M. Salisburg ◽  
Ashley L. Deline ◽  
Katrina W. Lexa ◽  
George C. Shields ◽  
Karl N. Kirschner
Keyword(s):  
Force Field ◽  
Molecular Dynamic ◽  
Molecular Dynamic Simulations ◽  
Dynamic Simulations

scholarly journals Integrated atomistic chemical imaging and reactive force field molecular dynamic simulations on silicon oxidation

2015 ◽  
Vol 106 (1) ◽  
pp. 011602 ◽  
Author(s):  
Santoshrupa Dumpala ◽  
Scott R. Broderick ◽  
Umedjon Khalilov ◽  
Erik C. Neyts ◽  
Adri C. T. van Duin ◽  
...  
Keyword(s):  
Force Field ◽  
Molecular Dynamic ◽  
Chemical Imaging ◽  
Molecular Dynamic Simulations ◽  
Reactive Force ◽  
Reactive Force Field ◽  
Silicon Oxidation ◽  
Dynamic Simulations

scholarly journals Challenges in modelling homogeneous catalysis: new answers from ab initio molecular dynamics to the controversy over the Wacker process

2014 ◽  
Vol 43 (14) ◽  
pp. 4940-4952 ◽  
Author(s):  
András Stirling ◽  
Nisanth N. Nair ◽  
Agustí Lledós ◽  
Gregori Ujaque
Keyword(s):  
Molecular Dynamics ◽  
Reaction Mechanism ◽  
Ab Initio ◽  
Molecular Dynamic ◽  
Homogeneous Catalysis ◽  
Experimental Results ◽  
Ab Initio Molecular Dynamics ◽  
Theoretical Treatment ◽  
Molecular Dynamic Simulations ◽  
Dynamic Simulations

The controversial reaction mechanism considering experimental results and theoretical treatment from static to ab initio molecular dynamic simulations is reviewed.

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