BLaDE: A Basic Lambda Dynamics Engine for GPU-Accelerated Molecular Dynamics Free Energy Calculations

2021 ◽  
Author(s):  
Ryan L. Hayes ◽  
Joshua Buckner ◽  
Charles L. Brooks
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Free Energy Calculations ◽  
Energy Calculations ◽  
Accelerated Molecular Dynamics

Integrating Multiple Accelerated Molecular Dynamics To Improve Accuracy of Free Energy Calculations

2018 ◽  
Vol 14 (3) ◽  
pp. 1216-1227 ◽  
Author(s):  
Xiangda Peng ◽  
Yuebin Zhang ◽  
Yan Li ◽  
QingLong Liu ◽  
Huiying Chu ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Free Energy Calculations ◽  
Energy Calculations ◽  
Accelerated Molecular Dynamics ◽  
Improve Accuracy

scholarly journals Insight into the Binding of DFG-out Allosteric Inhibitors to B-Raf Kinase Using Molecular Dynamics and Free Energy Calculations

2015 ◽  
Vol 11 (2) ◽  
pp. 124-136 ◽  
Author(s):  
Luis Coronel ◽  
Jose Granadino-Roldán ◽  
Marta Pinto ◽  
Maria Tomas ◽  
Maria Pujol ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Free Energy Calculations ◽  
Allosteric Inhibitors ◽  
Energy Calculations ◽  
Raf Kinase ◽  
Insight Into

Small-to-Large Length Scale Transition of TMAO Interaction with Hydrophobic Solutes

2021 ◽  
Author(s):  
Angelina Folberth ◽  
Swaminath Bharadwaj ◽  
Nico van der Vegt
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Md Simulations ◽  
Free Energy Calculations ◽  
Length Scale ◽  
Simulation Data ◽  
Energy Calculations ◽  
Large Length ◽  
Hydrophobic Solutes ◽  
Large Length Scale

We report the effect of trimethylamine N-oxide (TMAO) on the solvation of nonpolar solutes in water studied with molecular dynamics (MD) simulations and free-energy calculations. The simulation data indicate the...

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