Use of Umbrella Sampling in the Calculation of the Potential of Mean Force for Maltose in Vacuum From Molecular Dynamics Simulations

1995 ◽  
Vol 99 (29) ◽  
pp. 11339-11343 ◽  
Author(s):  
R. K. Schmidt ◽  
B. Teo ◽  
J. W. Brady
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Umbrella Sampling ◽  
Potential Of Mean Force ◽  
Dynamics Simulations

Umbrella sampling molecular dynamics simulations reveal concerted ion movement through G-quadruplex DNA channels

2017 ◽  
Vol 19 (18) ◽  
pp. 11017-11025 ◽  
Author(s):  
Parisa Akhshi ◽  
Gang Wu
Keyword(s):  
Molecular Dynamics ◽  
Ion Transport ◽  
Molecular Dynamics Simulations ◽  
Md Simulations ◽  
Umbrella Sampling ◽  
Potential Of Mean Force ◽  
Quadruplex Dna ◽  
Ion Movement ◽  
G Quadruplex ◽  
Dynamics Simulations

We have applied the umbrella sampling (US) method in all-atom molecular dynamics (MD) simulations to obtain potential of mean force (PMF) profiles for ion transport through three representative G-quadruplex DNA channels: [d(TG4T)]4, [d(G3T4G4)]2, and d[G4(T4G4)3].

Displacement of carbonates in Ca2UO2(CO3)3 by amidoxime-based ligands from free-energy simulations

2018 ◽  
Vol 47 (5) ◽  
pp. 1604-1613 ◽  
Author(s):  
Bo Li ◽  
Chad Priest ◽  
De-en Jiang
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Molecular Dynamics Simulations ◽  
Umbrella Sampling ◽  
Nacl Solution ◽  
Classical Molecular Dynamics ◽  
Energy Profiles ◽  
Energy Simulations ◽  
Dynamics Simulations ◽  
Free Energy Profiles

Classical molecular dynamics simulations coupled with umbrella sampling reveal the atomistic processes and free-energy profiles of the displacement of carbonate groups in the Ca2UO2(CO3)3 complex by amidoxime-based ligands in a 0.5 M NaCl solution.

scholarly journals Study of Ligand Binding Selectivity of Histone Deacetylases by Replica-Exchange Umbrella Sampling Molecular Dynamics Simulations

2016 ◽  
Vol 110 (3) ◽  
pp. 544a-545a
Author(s):  
Shuichiro Tsukamoto ◽  
Yoshitake Sakae ◽  
Yukihiro Itoh ◽  
Takayoshi Suzuki ◽  
Yuko Okamoto
Keyword(s):  
Molecular Dynamics ◽  
Ligand Binding ◽  
Molecular Dynamics Simulations ◽  
Histone Deacetylases ◽  
Umbrella Sampling ◽  
Replica Exchange ◽  
Binding Selectivity ◽  
Dynamics Simulations
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