scholarly journals Some connections between importance sampling and enhanced sampling methods in molecular dynamics

2017 ◽  
Vol 147 (19) ◽  
pp. 194107 ◽  
Author(s):  
H. C. Lie ◽  
J. Quer
Keyword(s):  
Molecular Dynamics ◽  
Importance Sampling ◽  
Sampling Methods ◽  
Enhanced Sampling

scholarly journals Using Long-Timescale Molecular Dynamics Simulations to Benchmark Enhanced Sampling Methods

2015 ◽  
Vol 108 (2) ◽  
pp. 183a
Author(s):  
Albert C. Pan ◽  
Thomas M. Weinreich ◽  
Stefano Piana ◽  
David E. Shaw
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Sampling Methods ◽  
Enhanced Sampling ◽  
Dynamics Simulations

The shuttling mechanism of foldaxanes: more than just translocation and rotation

2020 ◽  
Vol 22 (23) ◽  
pp. 12967-12972
Author(s):  
Peng Liu ◽  
Wenqi Hao ◽  
Xihui Bian ◽  
Donghai Mei
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Sampling Methods ◽  
Molecular Machines ◽  
Enhanced Sampling ◽  
Shrinkage And Swelling ◽  
Dynamics Simulations

Understanding movements within molecular machines is the prerequisite of tailoring its structure to achieve specific functions. With the aid of molecular dynamics simulations and enhanced sampling methods, movements within the foldaxane have been revealed. Movements, viz., translocation, rotation, tilt, shrinkage, and swelling, have been identified and investigated in detail.

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

New importance sampling methods for simulating sequential decoders

1993 ◽  
Vol 39 (5) ◽  
pp. 1716-1722 ◽  
Author(s):  
K.B. Letaief ◽  
J.S. Sadowsky
Keyword(s):  
Importance Sampling ◽  
Sampling Methods

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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