Comparing the Ability of Enhanced Sampling Molecular Dynamics Methods To Reproduce the Behavior of Fluorescent Labels on Proteins

2015 ◽  
Vol 11 (7) ◽  
pp. 3455-3465 ◽  
Author(s):  
Katarzyna Walczewska-Szewc ◽  
Evelyne Deplazes ◽  
Ben Corry
Keyword(s):  
Molecular Dynamics ◽  
Fluorescent Labels ◽  
Enhanced Sampling ◽  
Molecular Dynamics Methods

Drug Discovery and Molecular Dynamics: Methods, Applications and Perspective Beyond the Second Timescale

2017 ◽  
Vol 17 (23) ◽  
Author(s):  
Gerard Martínez-Rosell ◽  
Toni Giorgino ◽  
Matt J. Harvey ◽  
Gianni de Fabritiis
Keyword(s):  
Molecular Dynamics ◽  
Drug Discovery ◽  
Molecular Dynamics Methods

Steric and Electrostatic Effects on the Diffusion of CH4/CH3OH in Copper-Exchanged Zeolites: Insights from Enhanced Sampling Molecular Dynamics and Free Energy Calculations

Langmuir ◽  
2021 ◽  
Author(s):  
Luis Paulo M. Freitas ◽  
Anderson A. Espírito Santo ◽  
Tuanan C. Lourenço ◽  
Juarez L. F. Da Silva ◽  
Gustavo Troiano Feliciano
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Free Energy Calculations ◽  
Enhanced Sampling ◽  
Electrostatic Effects ◽  
Energy Calculations

Toward an Enhanced Sampling Molecular Dynamics Method for Studying Ligand-Induced Conformational Changes in Proteins

2015 ◽  
Vol 119 (46) ◽  
pp. 14594-14603 ◽  
Author(s):  
Ole Juul Andersen ◽  
Julie Grouleff ◽  
Perri Needham ◽  
Ross C. Walker ◽  
Frank Jensen
Keyword(s):  
Molecular Dynamics ◽  
Conformational Changes ◽  
Molecular Dynamics Method ◽  
Enhanced Sampling ◽  
Dynamics Method

Microstructure evolution and plastic deformation of Ni47Co53 alloy under tension

CrystEngComm ◽  
2022 ◽  
Author(s):  
ruibo ma ◽  
Lili Zhou ◽  
Yong-Chao Liang ◽  
Ze-an Tian ◽  
Yun-Fei Mo ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Plastic Deformation ◽  
Rapid Solidification ◽  
Microstructural Evolution ◽  
Microstructure Evolution ◽  
Cooling Rates ◽  
Solidification Processes ◽  
Molecular Dynamics Methods

To investigate microstructural evolution and plastic deformation under tension conditions, the rapid solidification processes of Ni47Co53 alloy are first simulated by molecular dynamics methods at cooling rates of 1011, 1012...

SPONGE : A GPU‐Accelerated Molecular Dynamics Package with Enhanced Sampling and AI‐Driven Algorithms

2021 ◽  
Author(s):  
Yu‐Peng Huang ◽  
Yijie Xia ◽  
Lijiang Yang ◽  
Jiachen Wei ◽  
Yi Isaac Yang ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Enhanced Sampling ◽  
Accelerated Molecular Dynamics

scholarly journals An Efficient GaMD Multi-Level Enhanced Sampling Strategy: Application to Polarizable Force Fields Simulations of Large Biological Systems

2021 ◽  
Author(s):  
Fréderic Célerse ◽  
Theo Jaffrelot-Inizan ◽  
Louis Lagardère ◽  
Olivier Adjoua ◽  
Pierre Monmarché ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Adaptive Sampling ◽  
Sampling Strategy ◽  
Umbrella Sampling ◽  
Potential Of Mean Force ◽  
Enhanced Sampling ◽  
Polarizable Force Field ◽  
Accelerated Molecular Dynamics ◽  
Polarizable Force Fields ◽  
Multi Level

We detail a novel multi-level enhanced sampling strategy grounded on Gaussian accelerated Molecular Dynamics (GaMD). First, we propose a GaMD multi-GPUs-accelerated implementation within the Tinker-HP molecular dynamics package. We then introduce the new "dual-water" mode and its use with the flexible AMOEBA polarizable force field. By adding harmonic boosts to the water stretching and bonding terms, it accelerates the solvent-solute interactions while enabling speedups thanks to the use of fast multiple--timestep integrators. To further reduce time-to-solution, we couple GaMD to Umbrella Sampling (US). The GaMD—US/dual-water approach is tested on the 1D Potential of Mean Force (PMF) of the CD2-CD58 system (168000 atoms) allowing the AMOEBA PMF to converge within 1 kcal/mol of the experimental value. Finally, Adaptive Sampling (AS) is added enabling AS-GaMD capabilities but also the introduction of the new Adaptive Sampling--US--GaMD (ASUS--GaMD) scheme. The highly parallel ASUS--GaMD setup decreases time to convergence by respectively 10 and 20 compared to GaMD--US and US.

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