An extended autoencoder model for reaction coordinate discovery in rare event molecular dynamics datasets

2021 ◽  
Vol 155 (6) ◽  
pp. 064103
Author(s):  
M. Frassek ◽  
A. Arjun ◽  
P. G. Bolhuis
Keyword(s):  
Molecular Dynamics ◽  
Rare Event ◽  
Reaction Coordinate

Fully Flexible Docking via Reaction-Coordinate-Independent Molecular Dynamics Simulations

2018 ◽  
Vol 58 (2) ◽  
pp. 490-500 ◽  
Author(s):  
Martina Bertazzo ◽  
Mattia Bernetti ◽  
Maurizio Recanatini ◽  
Matteo Masetti ◽  
Andrea Cavalli
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Reaction Coordinate ◽  
Flexible Docking ◽  
Dynamics Simulations

scholarly journals Wetting and cavitation pathways on nanodecorated surfaces

Soft Matter ◽  
2016 ◽  
Vol 12 (12) ◽  
pp. 3046-3055 ◽  
Author(s):  
Matteo Amabili ◽  
Emanuele Lisi ◽  
Alberto Giacomello ◽  
Carlo Massimo Casciola
Keyword(s):  
Molecular Dynamics ◽  
Rare Event ◽  
Cassie State

Rare event methods combined with molecular dynamics and macroscopic calculations reveal multiple pathways for the breakdown of the superhydrophobic Cassie state through wetting or cavitation.

scholarly journals Combining stochastic and deterministic approaches within high efficiency molecular simulations

2013 ◽  
Vol 11 (4) ◽  
Author(s):  
Bruno Escribano ◽  
Elena Akhmatskaya ◽  
Jon Mujika
Keyword(s):  
Molecular Dynamics ◽  
Monte Carlo ◽  
High Efficiency ◽  
Rare Event ◽  
Molecular Simulations ◽  
Monte Carlo Sampling ◽  
Symplectic Integrators ◽  
Computational Time ◽  
Hybrid Monte Carlo ◽  
Event Dynamics

AbstractGeneralized Shadow Hybrid Monte Carlo (GSHMC) is a method for molecular simulations that rigorously alternates Monte Carlo sampling from a canonical ensemble with integration of trajectories using Molecular Dynamics (MD). While conventional hybrid Monte Carlo methods completely re-sample particle’s velocities between MD trajectories, our method suggests a partial velocity update procedure which keeps a part of the dynamic information throughout the simulation. We use shadow (modified) Hamiltonians, the asymptotic expansions in powers of the discretization parameter corresponding to timestep, which are conserved by symplectic integrators to higher accuracy than true Hamiltonians. We present the implementation of this method into the highly efficient MD code GROMACS and demonstrate its performance and accuracy on computationally expensive systems like proteins in comparison with the molecular dynamics techniques already available in GROMACS. We take advantage of the state-of-the-art algorithms adopted in the code, leading to an optimal implementation of the method. Our implementation introduces virtually no overhead and can accurately recreate complex biological processes, including rare event dynamics, saving much computational time compared with the conventional simulation methods.

Crystal structure of adenylate kinase from an extremophilic archaeon Aeropyrum pernix with ATP and AMP

2020 ◽  
Vol 168 (3) ◽  
pp. 223-229
Author(s):  
Yoshinori Shibanuma ◽  
Naoki Nemoto ◽  
Norifumi Yamamoto ◽  
Gen-Ichi Sampei ◽  
Gota Kawai
Keyword(s):  
Crystal Structure ◽  
Molecular Dynamics ◽  
Quantum Mechanics ◽  
Reaction Mechanism ◽  
Adenylate Kinase ◽  
Reaction Coordinate ◽  
Amino Acid Residues ◽  
Aeropyrum Pernix ◽  
Adenylate Kinases

Abstract The crystal structure of an adenylate kinase from an extremophilic archaeon Aeropyrum pernix was determined in complex with full ligands, ATP-Mg2+ and AMP, at a resolution of 2.0 Å. The protein forms a trimer as found for other adenylate kinases from archaea. Interestingly, the reacting three atoms, two phosphorus and one oxygen atoms, were located almost in line, supporting the SN2 nucleophilic substitution reaction mechanism. Based on the crystal structure obtained, the reaction coordinate was estimated by the quantum mechanics calculations combined with molecular dynamics. It was found that the reaction undergoes two energy barriers; the steps for breaking the bond between the oxygen and γ-phosphorus atoms of ATP to produce a phosphoryl fragment and creating the bond between the phosphoryl fragment and the oxygen atom of the β-phosphate group of ADP. The reaction coordinate analysis also suggested the role of amino-acid residues for the catalysis of adenylate kinase.

scholarly journals Adaptive free energy sampling in multidimensional collective variable space using boxed molecular dynamics

2016 ◽  
Vol 195 ◽  
pp. 395-419 ◽  
Author(s):  
Mike O'Connor ◽  
Emanuele Paci ◽  
Simon McIntosh-Smith ◽  
David R. Glowacki
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Rare Event ◽  
Potential Of Mean Force ◽  
Good Evidence ◽  
Collective Variable ◽  
Rigid Body Dynamics ◽  
Free Energy Surface ◽  
Molecular Configuration ◽  
Free Energy Sampling

The past decade has seen the development of a new class of rare event methods in which molecular configuration space is divided into a set of boundaries/interfaces, and then short trajectories are run between boundaries. For all these methods, an important concern is how to generate boundaries. In this paper, we outline an algorithm for adaptively generating boundaries along a free energy surface in multi-dimensional collective variable (CV) space, building on the boxed molecular dynamics (BXD) rare event algorithm. BXD is a simple technique for accelerating the simulation of rare events and free energy sampling which has proven useful for calculating kinetics and free energy profiles in reactive and non-reactive molecular dynamics (MD) simulations across a range of systems, in both NVT and NVE ensembles. Two key developments outlined in this paper make it possible to automate BXD, and to adaptively map free energy and kinetics in complex systems. First, we have generalized BXD to multidimensional CV space. Using strategies from rigid-body dynamics, we have derived a simple and general velocity-reflection procedure that conserves energy for arbitrary collective variable definitions in multiple dimensions, and show that it is straightforward to apply BXD to sampling in multidimensional CV space so long as the Cartesian gradients ∇CV are available. Second, we have modified BXD to undertake on-the-fly statistical analysis during a trajectory, harnessing the information content latent in the dynamics to automatically determine boundary locations. Such automation not only makes BXD considerably easier to use; it also guarantees optimal boundaries, speeding up convergence. We have tested the multidimensional adaptive BXD procedure by calculating the potential of mean force for a chemical reaction recently investigated using both experimental and computational approaches – i.e., F + CD3CN → DF + D2CN in both the gas phase and a strongly coupled explicit CD3CN solvent. The results obtained using multidimensional adaptive BXD agree well with previously published experimental and computational results, providing good evidence for its reliability.

scholarly journals Prediction of enhanced solvent-induced enantioselectivity for a ring opening with a bifurcating reaction path

2015 ◽  
Vol 17 (13) ◽  
pp. 8372-8381 ◽  
Author(s):  
Barry K. Carpenter ◽  
Jeremy N. Harvey ◽  
David R. Glowacki
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Ring Opening ◽  
Reaction Path ◽  
Enantiomeric Excess ◽  
Reaction Coordinate ◽  
Dynamics Simulation

A fully atomistic molecular dynamics simulation predicts enhance induction of enantiomeric excess in the products of a reaction with a bifurcating reaction coordinate, when run in a chiral solvent.

Molecular Dynamics of Rare-Event Electrostatic Channeling

2021 ◽  
Vol MA2021-01 (28) ◽  
pp. 976-976
Author(s):  
Yan Xie ◽  
Scott Calabrese Barton
Keyword(s):  
Molecular Dynamics ◽  
Rare Event
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